Mouse methylome studies SRP590495 Track Settings

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mRNA-Engineered CRISPR-Cas Epigenetic Editors Enable Durable and Efficient Gene Silencing in Vivo [WGBS] [Hepa1-6, Liver]

Track collection: Mouse methylome studies

All tracks in this collection (604)

Common	Common methbase tracks for the mm39 assembly
DRP000505	Mouse DNA methylome (MethylC-seq) [ESC, Embryo, Sperm]
DRP000598	Mouse oocyte methylome [Oocyte]
DRP000638	Mouse PGC DNA methylome (PBAT) [Primordial Germ]
DRP002386	Methylome and gene expression of neonatal prospermatogonia and early postnatal undifferentiated and differentiating spermatogonia [Testes]
DRP003273	Methylome and transcriptome dynamics during mouse germ cell specification/differentiation in vitro
DRP003407	Software updates in the Illumina HiSeq platform affect whole-genome bisulfite sequencing [EpiLC, IMR90, Spermatogonia]
DRP003544	Mouse NS/PCs DNA methylome (PBAT) [Astrocyte, ESC, Neural Stem/Progenitor, Neuron, Oligodendrocyte]
DRP003670	Methylome of expanded mouse primordial germ cell-like cells [BVSC]
DRP004153	Mouse blactocyst methylome [Blastocyst, Parthenogenetic Blastocyst]
DRP004308	MIWI2 targets RNAs transcribed from piRNA-dependently methylated regions in mouse gonocytes [Gonocyte]
DRP006395	The role of DNMT3B in inflammation-related hepatocarcinogenesis
DRP008086	DNA methylation analysis of oocytes in a PCOS mouse model [Oocyte]
DRP008292	Whole genome bisulfite sequence of tissue and organoid
DRP008439	The DNMT3A ADD domain recognizing histone H3K4me0 is essential for processive DNA methylation and maternal imprinting in mouse oocytes [Embryo E10.5, Oocyte, Parthenogenesis Blastocyst]
DRP008539	Investigation of the effects of sperm DNA methylation disturbance by testicular histone hyperacetylation on the next generation in mouse [Sperm]
DRP010625	The identification of differentially methylated genes between hepatocytes and skeletal muscle of wild-type mice [Muscle]
DRP010881	Role of Tet3 in DNA demethylation in mouse SCNT embryos [SCNT embryo]
DRP011267	whole genome bisulfite sequencing of colon and colon-derived organoids [Colon, Colon-Derived Organoid]
DRP011537	Tracking hematopoietic stem cell aging reveals its heterogeneous composition [Bone Marrow]
DRP012798	The identification of differentially methylated genes between hepatocytes of wild-type and ob/ob mice
ERP001204	DNA_methylation_reprogramming_in_PGCs [ESC, Epiblast Cells, Primordial Germ]
ERP001632	B_Cell_Methylome [B Cells]
ERP001953	The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells [Epiblast, J1 ES, Primordial Germ]
ERP003744	DNMT3_KO_BS_seq [EPC, Epiblast]
ERP003907	Methylome_and_Hydroxymethylome_of_iPSC [ESC, MEF, iPSC]
ERP004116	Whole genome bisulfite sequencing of samples reprogramming to iPSC
ERP004476	Reprogramming_around_an_epigenetic_barrier_with_TET1 [EpiSC]
ERP005247	DNA methylation is required for the control of stem cell differentiation in the small intestine [Small Intestine]
ERP008742	Germ_cell_methylation_dynamics [308-D5 TE Embryo 1, 308-D5 TE Embryo 2, 693-D6 TE Embryo 2, A3 mPGCLC1, BS treated DNA PBAT library, C3 mPGCLC2, D2 mPGCLC1, D3 mPGCLC2, E3 mPGCLC2, ESC, F1 hPGCLC1, F2 mPGCLC1, F3 mPGCLC2, G2 mPGCLC1, G3 mPGCLC2, H3 mPGCLC2, P11(4), P14(2), P8(3), PRGp8 4, Passage 10 Sort 2, Passage 10 Sort 3, Passage 10 Sort 4, S6EOSKSR 1, S6EOSKSR 3, S6EOSp15 1, S6EOSp15 2, S6EOSp5 3, S6EOSp9 1, S6EOSp9 2, S6EOSp9 3, hES1, hES2, hES3, hEpiLC 2016214 2, hEpiLC 201635, hKSR2, hKSR3, mEpiLC E14 d1 1, mEpiLC E14 d2 2]
ERP010942	We present the first genome-scale analysis of the effect of CpG methylation on DNA-binding of TFs. [Embryo, GP5D, LHSAR cell with HOXB13 transduced, Lhsar, LoVo, VCap]
ERP012781	Mice deficient of Myc super-enhancer region reveal a differential control mechanism between normal and pathological growth
ERP015660	Quantifying epigenotype variations between mouse B and CD4+ T lymphocytes [Spleen]
ERP016240	Genome-wide DNA methylation landscape defines specialization of regulatory T cells in tissues [Liver, Skin]
ERP022031	Epigenetic regulation and transcriptional repression by Tet1 in the early post-implantation mouse embryo: WG Bisulfite sequencing [B6 incipient congenic (N5 >95% B6) epiblast-like]
ERP022077	A MILI independent piRNA biogenesis pathway residually loads MIWI2 empowering partial germline reprogramming activity. [Testis]
ERP107409	Defective germline reprogramming rewires the spermatogonial transcriptome [Testis]
ERP107948	DEEP data release for IHEC/EpiRR 2018 data freeze. [Fibroblast, Hepatocyte, Liver, White Adipocyte]
ERP110807	Methylation_profiles_in_cancer_induced_mouse_liver_tumours
ERP120304	Multi-omics characterization of MEK inhibitor resistant pancreatic cancer based on a genetically engineered mouse model-derived in vitro system
ERP126361	DNA methylation profiles of mouse sperm in response to antibiotic-induced gut microbiota dysbiosis using whole-genome bisulfite sequencing [Cauda Epididymal Sperm]
ERP128231	CpG island reconfiguration for the establishment and synchronization of polycomb functions upon exit from naive pluripotency [ESC]
ERP130901	Epigenomic rewiring of mouse hippocampus after resistance and endurance exercise training [Hippocampus]
ERP138895	Study of a mouse model of angioimmunoblastic T-cell lymphoma
ERP139499	Whole genome bisulfite sequencing of liver samples of five mammals (human, rhesus macaque, mouse, rat and dog) [Liver]
ERP155689	Whole Genome Bisulfite Sequencing of CLDN6High vs CLDN6Low Sorted EpiSCs and APSD, and WT vs Pbx1-KO EpiSCs [24h differentiation, Epiblast Cell]
ERP172394	Whole-genome oxidative bisulfite sequencing and data processing of mouse intestinal stem cells with old and young mitochondria [Small Intestine]
SRP004162	Dynamic epigenomic oscillations in differentiated cells
SRP007354	DNA binding factors shape the mouse methylome at distal regulatory regions [BIS_seq] [ES-derived neuronal progenitor, ESC]
SRP011945	Base Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome [ESC]
SRP013702	Dnmt3a protects active chromosome domains against cancer-associated hypomethylation [Lung]
SRP013703	GSE57230: Widespread contribution of transposable elements to the innovation of gene regulatory networks [mouse ENCODE] [Bone Marrow, Cerebellum, Cerebral Cortex, Embryonic Facial Prominence, Forebrain, Heart, Hindbrain, Intestine, Kidney, Large Intestine, Limb, Liver, Lung, Midbrain, Neural Tube, Olfactory Bulb, Small Intestine, Spleen, Stomach, Thymus]
SRP016893	Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells [ESC]
SRP017139	Dnmt2-dependent methylomes lack biologically relevant DNA methylation patterns [ESC]
SRP017350	Density and methylation state of CpG dinucleotides define histone variant specific retention of nucleosomes in mouse spermatozoa [Sperm]
SRP017503	Tissue-specific methylomes reveal epigenetic memory in adult mouse tissue [Bone Marrow, Cerebellum, Colon, Cortex, Heart, Intestine, Kidney, Liver, Lung, Olfactory Bulb, Pancreas, Placenta, Skin, Spleen, Stomach, Thymus, Uterus]
SRP017572	FGF Signaling Inhibition in ESCs Drives Rapid Genome-wide Demethylation to the Epigenetic Ground State of Pluripotency [ESC]
SRP018523	Bisulfite-Seq profiling of undifferentiated ESCs, and in vitro derived primordial germ cells (iPGCs) [ESCs-Rosa26-GFP, ESCs-V6.5, iPGCs, iPGCs-Rosa26-GFP, iPGCs-V6.5]
SRP018963	High resolution nulceotide level methylation map of female mouse primary keratinocytes [Primary Keratinocytes]
SRP019026	CG methylated microarrays identify novel methylated sequence bound by the CEBPB\|ATF4 heterodimer that are active in vivo [Primary Dermal Fibroblasts]
SRP020633	Mus musculus Epigenomics
SRP025152	Epigenetic and genetic changes during mouse hematopoietic stem cell aging [Bisulfite-Seq] [Murine bone marrow derived primary HSCs]
SRP025993	Maintenance of DNA methylation in embryonic stem cells depends on the histone H3K9 methyltransferases (K9 KO Methyl-Seq) [ESC]
SRP025996	Maintenance of DNA methylation in embryonic stem cells depends on the histone H3K9 methyltransferases (Dnmt3ab KO Methyl-Seq) [ESC]
SRP026048	Global epigenomic reconfiguration during mammalian brain development [Brain (Cerebral Cortex), Brain (Dorsal Prefrontal Cortex), Brain (Frontal Cortex), Brain (Middle Frontal Gyrus), ESC]
SRP026536	5mC Oxidation by Tet2 Modulates Enhancer Activity and Timing of Transcriptome Reprogramming during Differentiation [ESC]
SRP028709	Large conserved domains of low DNA methylation maintained by 5-hydroxymethycytosine and Dnmt3a [Bisulfite-Seq] [Murine bone marrow derived primary HSCs]
SRP028826	Gene expression and chromatin analysis of fused mouse-rat cells [Immortalized mouse Tail Fibroblast]
SRP029721	Genome-wide regulatory domains and their interactions in Mus musculus [Hematopoetic Stem Cell, splenic B cells]
SRP029902	Role of de novo DNA methyltransferases in hematopoietic stem cells (WGBS) [Murine bone marrow derived primary HSCs]
SRP032967	Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain (Bisulfite-seq) [Dentate Gyrus]
SRP033288	Dynamic DNA methylation in cardiac myocyte development, maturation and disease [Cardiac, Cardiac Myocyte]
SRP033304	The complete methylome of hematopoietic stem cells and their immediate progeny [HSC (LSK CD34-CD48-CD150+), MPP (LSK CD34+ CD48+ CD150-), MPP1 (LSK CD34+ CD48-CD150+), MPP2 (LSK CD34+ CD48+ CD150+)]
SRP034857	Large conserved domains of low DNA methylation maintained by 5-hydroxymethycytosine and Dnmt3a (CMS bisulfite-seq) [Murine bone marrow derived primary HSCs]
SRP037785	Two waves of de novo methylation during mouse germ cell development [Germ]
SRP039504	Single base resolution analysis of 5-formyl and 5-carboxyl cytosine reveals the actual promoter DNA methylation dynamics in embryonic stem cells [MAB-Seq] [ESC]
SRP040524	CG hypomethylation in Lsh-/- mouse embryonic fibroblasts is associated with de novo H3K4me1 formation and altered cellular plasticity [Cell Line, MEF]
SRP040627	Imprinted expression is different in visceral yolk sac and cystic embryoid body endoderm [Visceral Yolk Sac Endoderm]
SRP041083	Programming and inheritance of parental DNA methylomes in mammals [2-cell embryo, 4-cell embryo, E13.5 female PGC, E13.5 male PGC, E3.5 embryo, E6.5 embryo, E7.5 embryo, Inner Cell Mass, MII oocyte, Sperm]
SRP041257	Single-Cell Whole-Genome Bisulfite Sequencing for Analysis of Epigenetic Heterogeneity [ESC]
SRP041376	Tet proteins in DNA demethylation and cell fate restriction [Cell Line]
SRP041760	Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation [Bisulfite-Seq] [ESC]
SRP041847	Altered epigenetic programming links intestinal inflammation to colon cancer (Bisulfite-seq) [Colon]
SRP042360	Dnmt3L-histone H3 binding is necessary for male fertility and non-CG methylation [DNMT3 A/A, Wild Type]
SRP042409	Rlf, a widely-spaced zinc finger protein, is involved in maintaining epigenetic marks at CpG island shores and enhancer elements across the genome [Embryo, Liver]
SRP043370	Tet1 and Tet2 mediate epigenetic regulation of developmental genes by protecting DNA methylation canyons against hypermethylation [Bisulfite-Seq] [Embryonic Fibroblasts, Fibroblast]
SRP045054	The developmental potential of iPSCs is greatly influenced by the selection of the reprogramming factors [ESC, Induced Pluripotent Stem Cell]
SRP045179	Gender-specific post-natal demethylation and establishment of epigenetic memory [Liver]
SRP045747	Setdb1 is required for persistence of H3K9me3 and repression of endogenous retroviruses in mouse primordial germ cells [SSEA1+ primordial germ]
SRP047165	Distinct roles of DNMT1-dependent and –independent methylation patterns in the genome of mouse ES cells [ESC]
SRP047397	Genome-wide characterization of DNMT-deficient mouse ESCs reveals dynamicity of differentially-methylated-regions and its impact on bivalency composition [ES]
SRP049191	Single-base resolution analysis of active DNA demethylation using methylase-assisted bisulfite sequencing [ESC]
SRP049223	Transcription and Imprinting Dynamics in Developing Postnatal Male Germline Stem Cells [Spermatogonia]
SRP049674	Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain [Brain (Neocortex)]
SRP049697	DNA methylation status of Individual 4T1 Clonal Populations [Cell Line]
SRP049936	DNA methylation in mammalian placentas [Cerebrum, Cord Blood, Extraembryonic Membrane, Placenta, Trophoblasts]
SRP049965	MORC1 represses transposable elements in the mouse male germ line [Sorted Germ]
SRP050145	An alternative pluripotent state confers interspecies chimaeric competency [WGBS] [E5.75 derived EpiSCs, E5.75 derived rsEpiSCs]
SRP052235	HP1 is involved in regulating the global impact of DNA methylation on alternative splicing [ESC]
SRP055147	Maternal DNA methylation regulates early trophoblast development [Trophoblast]
SRP056705	An epigenetic memory of pregnancy in the mouse mammary gland [Mammary Gland]
SRP057157	Competition between DNA methylation and transcription factors determines binding of NRF1 [ESC]
SRP057505	Active DNA demethylation at enhancers during the vertebrate phylotypic period [Brain, Whole Embryo, sox10+]
SRP059433	Gender Differences in Global but not Targeted Demethylation in iPSC Reprogramming [BS seq AIDKO MEF1, BS seq ESC 1, BS seq ESC 2, BS seq ESC 3, BS seq P29 iPSC Clone1, BS seq d21 iPSC Clone3, BS seq d29 AIDKO iPSC Clone1, BS seq d29 AIDKO iPSC Clone2, BS seq d29 MALE iPSC Clone1, BS seq d29 MALE iPSC Clone2, BS seq d29 MALE iPSC Clone3, BS seq d29 iPSC Clone3, BS seq d6 SSEA1 positive 1, BS seq d6 SSEA1 positive 2, BS seq d6 SSEA1 positive 3, BS seq d6 Thy1 positive 1, BS seq d6 Thy1 positive 2, BS seq d6 Thy1 positive 3, BS seq d60 AIDKO iPSC Clone1, BS seq d60 MALE iPSC Clone1, BS seq d60 MALE iPSC Clone2, BS seq d60 MALE iPSC Clone3, BS seq d60 iPSC Clone2, BS seq d60 iPSC Clone3, Fibroblast, MEF, Reprogramming Fibroblast]
SRP059940	Chromatin dynamics and the role of G9a in gene regulation and enhancer silencing during early mouse development [Epiblast Stem Cell, Epiblast-Like]
SRP060643	De novo DNA methyltransferases DNMT3A and DNMT3B are essential of global DNA methylation maintenance [BS-Seq] [ESC]
SRP060646	De novo DNA methyltransferases DNMT3A and DNMT3B are essential of global DNA methylation maintenance [TAB-Seq] [ESC]
SRP060660	MIWI2 and MILI have differential effects on piRNA biogenesis and DNA methylation [MACS sorted (a-EpCAM G8.8 antibody sc-53532) spermatocytes]
SRP061339	Sequence Features Accurately Predict Genome-wide MeCP2 Binding in vivo [Olfactory Epithelium]
SRP061876	An epigenetic switch ensures transposon repression upon acute loss of DNA methylation in ES cells (WGBS) [J1 WT mouse ES]
SRP062482	TET proteins regulate lineage specification and TCR-mediated expansion of iNKT cells (WGBS) [iNKT cells]
SRP062557	DNMT3A and TET2 Compete and Cooperate to Repress Differentiation Lineage-Specific Factors in Hematopoietic Stem Cells [Tet2 and Dnmt3a double knockout Hematopoietic stem cell, Tet2 knockout Hematopoietic stem cell]
SRP062575	Genetic and epigenetic variation among inbred littermates: identification of metastable epialleles in the mouse [Liver]
SRP062705	Whole genome bisulfite sequencing of sperm from a mouse heterozygous for a mutation in Setdb1 (MommeD13) and a wildtype mouse. [Sperm]
SRP063015	Epigenomic Landscapes of Retinal Rods and Cones [Retina]
SRP063093	Acute loss of TET function results in aggressive myeloid cancer in mice [WGBS] [LSK]
SRP063275	New roles for DNA cytosine modification, eRNA, anchors and super-anchors in developing B cell progenitors [Rag1 deficient pro-B, Tcf3(E2A) deficient pre-pro-B]
SRP063453	Unique Broad Histone Lysine 4 Methylation Domains in Mouse Oocytes and Dynamic Regulation during Maternal to Zygotic Transition [P12 oocyte, P15 oocyte]
SRP065034	Mus musculus and Mus spretus sperm methylation [Testis]
SRP065509	Trans-effects of sub-chromosomal duplications on DNA methylation patterns in mouse models of Down syndrome: whole genome bisulfite sequencing of cerebral samples from Dp(10)1Yey and Dp(16)1Yey mouse models. [Whole cerebral hemispheres (with meninges removed)]
SRP065556	Dynamic Changes in Histone Modifications Precede de novo DNA Methylation in Oocytes [Oocyte]
SRP066668	genomic DNA from MEF cells [Cultured MEF]
SRP067094	Chromatin decompaction coupled MuERVL endogenous retrovirus activation induces genome-wide DNA demethylation [ESC]
SRP067341	DNA methylation oscillations at CpG poor enhancers in primed embryonic stem cells [PBAT Bisfulfite-seq] [ESC]
SRP067447	Genetic and Epigenetic Variation, but Not Diet, Shape the Sperm Methylome [Cauda Epididymis And Vas Deferens]
SRP068043	Dynamic epigenomic landscapes during early lineage specification in mouse embryos [ESC, Ectoderm, Endoderm, Epiblast, Inner Cell Mass, Mesoderm, Primitive Streak, Trophectoderm, Visceral Endoderm]
SRP068730	Epigenetic reprogramming enables the primordial germ cell-to-gonocyte transition (WGBS) [PGC]
SRP069120	Mus musculus strain:C57BL/6 Epigenomics [Liver, MEFs in culture]
SRP069139	ZFP57 maintains the parent-of-origin-specific expression of the imprinted genes and differentially affects non-imprinted targets in mouse embryonic stem cells (BS-seq and RRBS) [ESC]
SRP069154	Isoform switch of TET1 regulates DNA demethylation and mouse development [ESC]
SRP070637	Single-cell multi-omics sequencing of mouse early embryos and embryonic stem cells [ESC]
SRP070642	Methylation and gene expression profiling in Dnmt3a-deficient chronic lymphocytic leukemia and peripheral T-cell lymphoma in mice. [Spleen]
SRP071233	Iron-Heme-Bach1 Axis Is Involved In Erythroblast Adaptation To Iron Deficiency [erthroblast (Bach1 KO), erthroblast (WT)]
SRP071782	Mammalian sperm exhibit epigenetic priming of embryonic and adult regulatory landscapes (BS-Seq) [Sperm]
SRP074072	WGBS assessment of global methylation alterations in Dnmt3aKO/FLT3-ITD lymphoid leukemia [Leukemic, Murine thymus derived CD4/CD8 double positive T cells]
SRP074379	Genome-wide map of DNA methylation to unravel the function of EBF1 C-terminus domain [Fetal Liver]
SRP075309	Mus musculus Epigenomics [ES]
SRP075981	GEO accession GSE82125 is currently private and is scheduled to be released on May 30, 2017. [ES-derived neural progenitor, ESC]
SRP076056	Role of Tet proteins in B cell development [Pro B cells]
SRP077875	Allele-Specific Non-CG Methylation Marks Domains of Active Chromatin in Mouse Brain [Brain (Prefrontal Cortex)]
SRP077894	Single base resolution of the complete 5-mC and 5-hmC cardiac methylome in heart failure [Whole Heart]
SRP078059	The de novo DNA methyltransferase DNMT3C protects male fertility from transposon activity (Bisulfite-seq). [10 dpp total germ]
SRP078072	Derivation of ground-state female ESCs maintaining gamete-derived DNA methylation [ESC]
SRP078328	Epigenetic restriction of embryonic and extraembryonic lineages mirrors the somatic transition to cancer (WGBS) [Extraembryonic Ectoderm, Inner Cell Mass, Trophectoderm, precompacted 8 cell stage embryos, proximal Epiblast]
SRP078445	DNA Methylation Divergence and Tissue Specialization in the Developing Mouse Placenta [Whole Placenta]
SRP078848	Whole genome bisulfite and TAB-Sequencing from sorted neurons in the adult mouse brain [Brain]
SRP078871	Whole genome bisulfite sequencing of adult hypothalamus male mouse brain [Hypothalamus Region From Brain]
SRP078942	Cis-regulatory landscape of four cell types of the retina [Cones, Horizontal Cells, Rods, Starbust Amacrine]
SRP080866	DNA methyltransferase 3b regulates articular cartilage homeostasis by altering chondrocyte metabolism [Primary Articular Chondrocytes]
SRP081004	Postnatal DNA demethylation and its role in tissue maturation [Hepatocyte]
SRP081133	DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumour immunotolerance [WGBS] [Inner Cell Mass]
SRP081312	DNA methylation regulates intron retention via altered MeCP2-mediated splicing factor recruitment [Blood]
SRP081475	Methylomes of wild-type and MeCP2 knockout brain cells [Brain]
SRP082360	Epigenetic memory of obesity in mouse colonic epithelium [Colon]
SRP083753	LKB1 loss links the serine metabolic network to DNA methylation and tumourigenesis [bisulfite-seq] [Pancreas]
SRP083895	Transcription and chromatin determinants of the rate of de novo DNA methylation in oocytes [Oocyte]
SRP089825	Enhanced Pluripotent Cell Function through miR-203-mediated Control of DNA Methylation [Ebs from iPs WT (10 days of differentiation), Ebs from iPs miR-203 KI-N5 + DOX, Ebs from iPs miR-203 KI-N9 + DOX, iPs WT long after DOX, iPs WT short after DOX, iPs WT t=0, iPs miR-203 KI-N5 (t=0), iPs miR-203 KI-N5 long after DOX, iPs miR-203 KI-N5 short after DOX, iPs miR-203 KI-N9 (t=0), iPs miR-203 KI-N9 long after DOX, iPs miR-203 KI-N9 short after DOX]
SRP089858	A novel requirement for Drosha in maintenance of mammalian CG methylation [ESCs (ES cells)]
SRP090139	Analyzing whole genome bisulfite sequencing data from highly divergent genotypes [Liver]
SRP090219	The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis [WGBS_Mm] [ESC, Embryonic Fibroblasts, Retina, derived iPSCs fMG02, derived iPSCs fMG03, immature retinal-derived iPSCs 8601, mature retinal-derived iPSCs 3302, mature retinal-derived iPSCs 7602]
SRP090249	Whole Genome Bisulfite Sequencing in Pax7-reprogrammed corticotropes AtT-20 cells [Pituitary Corticotroph]
SRP090505	DNA methylation profiling of vascular maturation [Lung]
SRP090698	Epigenetic Memory Underlies Cell Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells [Lks Slam]
SRP090852	Vitamin C induced epigenomic remodeling in IDH1 mutant acute myeloid leukemia [HOXA9 immortalized bone marrow]
SRP091011	Tracking of dCas9-methyltransferase footprints [ESC]
SRP091938	Increased H3K9 methylation and impaired expression of Protocadherins are associated with the cognitive dysfunctions of the Kleefstra syndrome [Brain]
SRP092244	Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions (WGBS 1) [Hepatocytes]
SRP092247	Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions (WGBS 2) [Hepatocytes]
SRP092540	WGBS assessment of global methylation alterations in hematopoietic stem and progenitor cells [methyl-seq] [Intermediate-Term Hematopoietic Stem Cell, Long-Term Hematopoietic Stem Cell, Multi-Potent Progenitor, Short-Term Hematopoeitic Stem Cell]
SRP094653	ncRNA transcription-induced changes in nuclear architecture directs with high precision enhancer-promoter interaction [in-vitro DN2]
SRP095235	Dietary restriction protects from age-associated DNA methylation and induces epigenetic reprogramming of lipid metabolism [Liver]
SRP095627	DNA methylomes at base resolution of mouse embryonic fibroblasts in G1 and G2 phase of cell cycle [MEF]
SRP097054	DNA methylation of SAMP8 and SAMR1 mice [Cerebral?Cortex]
SRP097617	MLL2 conveys transcription-independent H3K4me3 in the oocyte [Germinal Vesicle Oocytes]
SRP099007	Microglia isolated from juvenile offspring of dams with allergic asthma exhibit methylation and transcriptional alterations to autism risk genes [WGBS] [Brain]
SRP099066	The BLUEPRINT Murine Lymphocyte Epigenome Reference Resource. [Whole Genome Bisulfite-Seq] [CD4+CD62L+ T cells, CD43-B cells]
SRP099067	The BLUEPRINT Murine Lymphocyte Epigenome Reference Resource. [Whole Genome Bisulfite-Seq_OX] [CD4+CD62L+ T cells, CD43-B cells]
SRP100972	5-hydroxymethylcytosine Accumulation in Postmitotic Neurons Results in Functional Demethylation of Expressed Genes [MethylC-Seq and oxBS-Seq] [Cerebellar Granule Cells]
SRP101416	Whole-genome bisulfite-seq (WGBS) on Lin-Sca1+Kit+ (LSK) bone marrow cells from wild-type C57BL/6J mice [Lin-Sca1+Kit-cells]
SRP101453	Environmental enrichment increases transcriptional and epigenetic differentiation between mouse dorsal and ventral dentate gyrus neurons [Brain (Dentate Gyrus Of The Hippocampus)]
SRP101591	Simultaneous mapping of active DNA demethylation and sister chromatid exchange in single cells [Around 100 mouse ESCs E14]
SRP101774	Isoform-specific localization of DNMT3A regulates DNA methylation fidelity at bivalent CpG islands [WGBS] [ESC]
SRP103077	Mapping DNA methylation and CTCF/cohesin occupancy on nascent chromatin and DNMT-targeted nascent chromatin [ESC]
SRP103763	Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the mouse brain [Cerebellum, Cortex, Olfactory Bulb]
SRP105210	Loss of Dnmt3a Immortalizes Hematopoietic Stem Cells in vivo [WGBS] [Hematopoietic Stem Cell]
SRP105270	Reprogramming of H3K9me3-dependent heterochromatin during mammalian early embryo development [WGBS] [4-cell embryo, 6.5 day embyo epiblast, 6.5 day embyo extraembryonic ectoderm, 7.5 day embyo epiblast, 7.5 day embyo extraembryonic ectoderm, 8-cell embryo, Inner Cell Mass, Morula Embro, Trophoblast, Zygote, early 2-cell embryo, late 2-cell embryo]
SRP106356	Activation of Lineage-Regulators and Transposable Elements Across a Pluripotent Spectrum [2i N2B27 BL6, 2i/LIF GMEM/10% KSR BL6, 2i/LIF GMEM/10% serum 129, 2i/LIF N2B27 BL6, Ch/LIF N2B27 BL6, Pd/LIF N2B27 BL6, Serum/LIF Feeders GMEM BL6, Serum/LIF GMEM 129]
SRP108295	De novo epigenetic programs inhibit PD-1 blockade-mediated T-cell rejuvenation [WGBS] [Antigen-specific CD8 T cells, Naive CD8 T cells]
SRP108349	Enhancing the Potency of Mouse Embryonic Stem Cells [BS-Seq] [ESC]
SRP108476	Whole genome bisulfite sequencing of Ing1/Gadd45a double knockout and wildtype mouse embryonic fibroblasts [MEF]
SRP109758	Cytosine methylation dynamics during spermatogenesis and post-testicular sperm maturation [Primary, Sperm]
SRP109785	Paternal cold exposure enhances brown adipose tissue sensitivity in offspring and ameliorates diet induced obesity [Sperm]
SRP109867	Base-resolution analysis of DNA methylation patterns downstream of Dnmt3a in mouse naïve B cells [Spleen]
SRP110902	DNMT3A haploinsufficiency predisposes hematopoietic cells to myeloid malignancies [Bone Marrow]
SRP111167	DNA methylation dynamics during embryonic development and postnatal maturation of the auditory organ of Corti [Organ Of Corti]
SRP111382	WGBS assessment of global methylation alterations in Dnmt3aKO or Dnmt3bKO mouse embryonic stem cells [ESC]
SRP111384	rahu is a mutant allele of Dnmt3c, encoding a DNA methyltransferase homolog required for meiosis and transposon repression in the mouse male germline [WGBS] [Whole Testis]
SRP111470	Whole genome bisulfite sequencing of mouse neural progenitor cells and neurons from the mouse cerebral cortex at day 15.5 of embryonic development [Cortical Neurons, Neural Progenitor]
SRP113186	Integrative Proteomic Profiling Reveals PRC2-Dependent Epigenetic Crosstalk Maintains Ground-State Pluripotency. [ESC]
SRP113409	Transcriptional and epigenetic profiling of aged mouse SVZ-derived neural stem / progenitor cells [SVZ-derived neural stem / progenitor]
SRP113417	Chromatin and Transcriptional Dynamics in Adult Germline Stem Cells and Mammalian Spermatogenesis [Spermatogonia (Thy1+), Testis]
SRP113606	Transient and permanent reconfiguration of chromatin and transcription factor occupancy drive reprogramming [MEF, MEF derived induced pluripotent stem cell, day12 MEF reprogramming intermediates, day3 MEF reprogramming intermediates, day6 MEF reprogramming intermediates, day9 MEF reprogramming intermediates]
SRP115607	A role of Polycomb in the maintenance of hypomethylation for DNA methylation valley [ESC]
SRP116373	Early-life gene expression in neurons modulates lasting epigenetic states. [Bisulfite-seq] [Cortex, Hippocampus]
SRP116554	Snord116-dependent diurnal rhythm of DNA methylation in mouse cortex [Cerebral Cortex]
SRP117079	Transcription factors drive Tet2-mediated enhancer demethylation to reprogram cell fate [Bisulfite-Seq] [Bone Marrow, Embryo (Inner Cell Mass), Inner Cell Mass]
SRP118911	High-Resolution Dissection of Conducive Somatic Cell Reprogramming to Naïve Ground State Pluripotency in Mbd3/NuRD and Gatad2a/NuRD Depleted Systems [WGBS] [Gatad2a-/-cell line, Mbd3f/-cell line, WT cell line]
SRP119143	Transcriptomic and epigenomic analysis during conversion from mouse microglia into induced-neuronal (iN) cells [Cortex]
SRP119366	Long genes linked to autism harbor intragenic super-enhancer-like chromatin domains [Cortical Excitatory Neurons]
SRP119705	DNA hypermethylation encroachment at CpG island borders in cancer is predisposed by H3K4 monomethylation [WGBS_Mm] [Spleen bulk B cells, blood (B cell-depleted)]
SRP123210	Genetics, sex and life experience influence DNA methylation in the mouse [Liver]
SRP123612	Novel Principles of Cellular Reprogramming Revealed by Prospective Isolation and Characterization of Rare Intermediates Poised to Generate iPSCs [WGBS] [MEF, Reprogramming Intermediate, iPSC]
SRP125227	Next Generation Sequencing for Genome-wide Maps of DNA Methylaton in mES Cells [ESC]
SRP125320	Effector CD8 T cells dedifferentiate into long-lived memory cells [Acute GP33-specific CD8 T cells, Acute Memory Precursor P14, Acute Terminal Effector P14, P14 CD8 T cells]
SRP125421	Dynamic EBF1 occupancy directs sequential epigenetic and transcriptional events in B cell programming [Bisulfite-Seq-Cre] [Ebf1-deficient B cell progenitors]
SRP125690	Forniceal deep brain stimulation induces gene expression and splicing changes that promote neurogenesis and synaptic plasticity [Dentate Gyrus]
SRP126875	Differences in cell cycle status underlie transcriptional heterogeneity in the HSC compartment [HSC]
SRP127685	Setd2 deficiency impairs hematopoietic stem cell self-renewal and causes malignant transformation [Bone marrow LSK]
SRP127792	Single-cell dissection of long non-coding RNAs pivotal for embryonic hematopoietic stem cell development [T1 pre-HSC]
SRP130993	SCNT embryos are defective for H3K27me3 imprinting [RNA-seq] [Blastocysts Generated With Somatic Nuclear Transffer]
SRP131922	Analysis of genetically diverse macrophages reveals local and domain-wide mechanisms that control transcription factor binding and function [bone marrow derived macropages (BMDM)]
SRP132683	DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries [ESC]
SRP133323	Extensive recovery of embryonic enhancer and gene memory stored in hypomethylated enhancer DNA. [Intestinal Villus, Midgut Epithelial]
SRP133565	Genome-wide identification of distinct target loci for de novo DNA methylation by DNMT3A and DNMT3B during mammalian development [MEF]
SRP133698	Global DNA methylation remodeling during direct reprogramming from fibroblast to neuron [MethylC-seq] [Direct reprogramming from fibroblast to neuron induced with Ascl1 for 2 days, Direct reprogramming from fibroblast to neuron induced with Ascl1 for 22 days, Direct reprogramming from fibroblast to neuron induced with Ascl1 for 5 days, Direct reprogramming from fibroblast to neuron induced with BAM for 22 days, Direct reprogramming from fibroblast to neuron induced with BAM for 5 days, Embryonic Fibroblast, Neural Progenitor, Neural progenitor cells differentiated for 14 days, Neural progenitor cells differentiated for 21 days, Neural progenitor cells differentiated for 7 days]
SRP135700	Transcriptional and Epigenomic Landscapes of CNS and non-CNS Vascular Endothelial Cells [Brain, Kidney, Liver, Lung]
SRP136257	Mammalian ISWI and SWI/SNF selectively mediate binding of distinct groups of transcription factors (Bis-seq data sets) [ESC]
SRP136419	WGBS assessment of global methylation alterations in Dnmt3a1KO , Dnmt3a2KO, Dnmt3aKO, Tet1KO and DKO mouse embryonic stem cells [ESC]
SRP136449	Comprehensive analysis of H3K9me2 oocytes, together with DNA methylation and expression analysis of G9a conditional KO oocytes and maternal KO preimplantation embryos [Blastocysts, Embryo, Oocyte]
SRP136786	Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution [E14 mouse ESCs]
SRP139083	DNA 5-methylcytosine specific profiling with limited input [ESC]
SRP139795	Transient reduction of DNA methylation at the onset of meiosis in male mice [Testis]
SRP142028	Mus musculus Epigenomics [MEF]
SRP149052	Single-Cell RNA-Seq Reveals Dynamic Early Embryonic-like Programs during Chemical Reprogramming [CiPSCs, Intermediate, XEN-like]
SRP151020	Inhibition of aberrant DNA re-methylation improves development of cloned embryos (WGBS-Seq) [Cumulus, Embryonic Fibroblast Cell, Nuclear Transfer Embryo, Sertoli]
SRP151137	DNA methylation oscillations at CpG poor enhancers in primed embryonic stem cells [scRNA-Seq, scBS-Seq] [Embryo]
SRP151590	Integrated Genomic Analysis of a Stem Cell Model of Overgrowth Syndrome with Intellectual Disability (WGBS) [J1 ESC, J1 NSC]
SRP151725	Imprecise DNMT1 activity coupled with neighbor-guided correction enables robust yet flexible epigenetic inheritance [ESC, mESC-derived]
SRP154319	Effects of environmental enrichment on postnatal mouse cortex regulome [Brain Cortex]
SRP154996	Epigenetic changes of the thioredoxin system in the tx-j mouse model and in patients with Wilson disease [Liver]
SRP155404	A DNMT3A PWWP mutation leads to methylation of bivalent chromatin and postnatal growth retardation in mice [Epiblast, Hypothalamus, Liver]
SRP156136	MethMotif: An integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles [Colon, Spleen]
SRP156779	DNA hypermethylation encroachment at CpG island borders in cancer is predisposed by H3K4 monomethylation [mESC_WGBS] [ESC]
SRP158409	H3K36me2 recruits DNMT3A and shapes intergenic DNA methylation landscapes [C3H embryo-derived mesenchymal progenitor, C57BL/6 x 129S4/SvJae F1 embryo-derived ESCs, Patient-derived head and neck squamous cell carcinoma cell line]
SRP158977	Methylome assays of E14.5 pancreatic progenitor cells [Endocrine Enrichment]
SRP159191	Long-range epigenetic concordance revealed by simultaneous profiling of DNA methylation and chromosomal conformation changes in bulk and single cell Methyl-HiC [ESC]
SRP159665	WGBS (Whole Genome Bisulfite Sequencing) of Wild-type and Math5-/- mouse dLGN (dorsolateral geniculate nucleus) at postnatal day 6 and postnatal day 23 [Brain]
SRP160386	Perturbation of the OGT-TET1 interaction in mouse embryonic stem cells (WGBS) [Tet1 D2018A mutant knock in mouse stem cell, Wild Type Mouse Stem Cell]
SRP161525	True 5-methylcytosine profiling of late reprogramming stages during in vitro reprogramming of mouse embryonic fibroblasts (MEFs) to induced pluripotent stem cells (iPSCs) [Day 10 totalx2 mCherry+/GFP+, Day 10 totalx2 mCherry+/GFP-, Day 12 naivex2 mCherry+/GFP+, Day 12 naivex2 mCherry+/GFP-, Day 14 naivex2 mCherry+/GFP+, Fibroblast, TET1 KO iPSC clonal line experiment 1, TET1 KO iPSC clonal line experiment 2, wild-type iPSC clonal line experiment 1, wild-type iPSC clonal line experiment 2]
SRP162035	Activin A and BMP4 Signaling Expands Potency of Mouse Embryonic Stem Cells in Serum Free Media [ESC, Epiblast Stem Cell]
SRP162771	Characterization of the DNA methylome in retinal pigment epithelium (RPE) of adult mice [retinal pigment epithelium (RPE)]
SRP163215	Aging of mouse spermatogonial stem cells by Wnt7b-Jnk pathway activation [Bisulfite-seq] [Testis]
SRP165997	Dynamic enhancer partitioning instructs Zdbf2 activation during epigenetic reprogramming [bisulfite-seq] [Epiblast-like]
SRP167689	WGBS in wild-type and MommeD1mut MEFs [MEF]
SRP167718	Next Generation Sequencing Combined Analysis of DNA Methylome and Transcriptome Reveal Novel Candidate Genes of Neuroprotective with Response to Ischemic Preconditioning [Brain]
SRP168345	Characterization of the DNA methylome in murine Müller glia [Retina]
SRP168393	DNA methylation in AgRP neurons regulates voluntary exercise behaviour in mice [Neuron]
SRP168427	Tet inactivation disrupts YY1 binding and long-range chromatin interactions to cause developmental defects in embryonic heart [Embryonic Heart]
SRP170065	Differential roles of Stella in the modulation of DNA methylation during oocyte and zygotic development [Female Pronucleus, Male Pronucleus, Oocyte]
SRP171165	Transcriptonal and epigenetic changes of adult liver cells in vivo and in vitro [Adult DDC damaged liver, Adult Healthy Liver]
SRP172778	GR mutation in mice changes the genome-wide epigenome of frontal cortex in a highly sex-specific manner [Frontal Cortex]
SRP173239	DNA methylation estimation using methylation-sensitive restriction enzyme bisulfite sequencing (MREBS) [ESC, Embryonic Fibroblasts]
SRP173926	Loss of non-CpG methylation in inhibitory neurons impairs neural function through a mechanism that partially overlaps with Rett syndrome [Whole Striatum]
SRP174096	Endogenous retroviral insertions drive non-canonical imprinting in extra-embryonic tissues [Bisulfite-Seq] [Epiblast, Extra-embryonic ectoderm]
SRP174255	Effects of combined treatment of EGCG and environmental enrichment on postnatal mouse cortex regulome [Brain Cortex]
SRP174491	FoxA-dependent demethylation of DNA initiates epigenetic memory of cellular identity [Hepatocytes]
SRP174666	Super-enhancer subregions highly bound by the nuclear receptor ESRRB regulate the exit from naïve pluripotency [Epiblast Stem Cells (EpiSCs)]
SRP174993	ChIP-seq and RNA-seq analysis of histone Kcr in the embryonic forebrain and neural stem/progenitor cells. [Forebrain]
SRP176417	Single cell multi-omics analysis reveals novel roles for DNA methylation in sensory neuron injury responses [Neuron]
SRP178652	Branched-chain Amino Acid Aminotransferase-1 Regulates Self-Renewal and Pluripotency of Mouse Embryonic Stem Cells through Ras Signaling [mES]
SRP183094	The intestinal microbiota programs DNA methylation to control tissue homeostasis and inflammation [BiSulfite-seq] [Colon Epithelial]
SRP184524	RNA m6A modification mediated by METTL3 is important for IAP heterochromatin integrity in mESCs (WGBS) [ESC]
SRP185723	WGBS of WT and Smchd1-KO ES cells [ESC]
SRP185738	Characterization of the DNA methylome in embryonic retina, retinal progenitors, and RGCs [Retina]
SRP186631	Epigenetic signatures of chronic social stress in stress-susceptible animals [Nucleus Accumbens]
SRP186642	Genome-wide methyl-cytosine competition by DNMT and TET [ESC, EpiSCs, In Vitro Derived Motor Neurons]
SRP186720	Association Between Early Life DNA Methylation Patterns with Age-Related Transcriptional Changes [Hippocampus]
SRP187205	Methylome profiling of GADD45 deficient mouse embryonic stem cells [ESCs (mESC)]
SRP188205	MeCP2 represses the rate of transcriptional initiation of highly methylated long genes (BS-Seq and OxBS-Seq) [Forebrain]
SRP188734	Downregulation of Uhrf1 activity by TGF-ß signaling controls Foxp3 methylation and iTreg cell differentiation [Lymph Nodes]
SRP189864	Uncoupling histone H3K4 trimethylation from developmental gene expression via an epigenetic equilibrium of Polycomb, COMPASS and DNA methylation [ESC]
SRP191868	Genome-wide analysis of DNA methylation profile in astrocytes isolated from naïve mice or EAE mice transduced with astrocyte-specific Mafg-targeting or non-targeting lentiviruses [WGBS] [Flow Cytometry Sorted Astrocytes]
SRP192143	Setd2 deficiency impaired erythroid differentiation and accelerated Myelodysplastic Syndrome(MDS) - associated leukemogenesis through S100A8 and S100A9 [Bone Marrow, Spleen]
SRP193267	Allelic histone-to-DNA methylation switch establishes secondary DMR to maintain noncanonical imprinting [E6.5 extraembryonic ectoderm]
SRP194541	Whole genome bisulfite genome analysis of OX40L-Jagged-1 expanded Treg and Teff cells [Spleen]
SRP195507	Genome-wide roles of DNA methyltransferases in mouse embryos [Whole Embryos]
SRP198282	Hammer-seq to measure kinetics of DNA methylation maintenance in HeLa cells [Cervix, Inner Cell Mass]
SRP199205	Tox reinforces the phenotype and longevity of exhausted T-cells in chronic viral infection [Bisulfite-Seq] [P14 T-cells]
SRP201955	Analysis of dendritic cell differences [Bone Marrow]
SRP212622	Profiling of DNA Methylation during RANKL Induced Osteoclastogenesis using Whole-Genome Bisulfite Sequencing [Bone Marrow]
SRP212761	Single-cell methylation and accessibility of mouse embryos E6.5 and E7.5. Second batch. [E7.5 embryo]
SRP214596	Dnmt3a and Dnmt3b-mediated decommissioning of fetal enhancers linked to kidney disease [Kidney]
SRP215028	Paradoxical association of TET loss of function with genome-wide hypomethylation [iNKT]
SRP216390	Epigenetic and transcriptional changes in aging mouse rod photoreceptors [WGBS] [Rod Photoreceptors]
SRP217940	Bivalent promoter hypermethylation in cancer is linked to the H327me3/H3K4me3 ratio in embryonic stem cells [ES]
SRP219391	Maternal exposure to a mitochondrial toxicant results in life-long alterations in DNA methylation and gene expression in the offspring [Liver]
SRP221485	Epigenetic regulator function through mouse gastrulation [Extraembryonic Ectoderm, proximal Epiblast]
SRP222128	Genome-wide analysis of methylated DNA in control and Tet2/Tet3-deficient B cells [Primary B cells]
SRP222566	Whole genome bisulfite Sequencing data of four types mouse spermatogenesis [Testis]
SRP223436	Unique Transcription Factor Functions Regulate Epigenetic and Transcriptional Dynamics During Cardiac Reprogramming [alphaMHC-GFP+ sorted induced cardiomyocytes, dsRed+ sorted fibroblasts (control infection)]
SRP223513	G9a plays distinct roles in maintaining DNA methylation, retrotransposon silencing and chromatin looping [ESC]
SRP227031	EED is required for Mouse Primordial Germ Cell Differentiation in the Embryonic Gonad [Primordial Germ]
SRP229336	DeepH&M: Simultaneous determination of single-CpG hydroxymethylation and methylation levels from enrichment and restriction enzyme sequencing methods [Cerebellum, Cortex]
SRP229373	Novel Isoforms of the Epigenetic Regulator TET1 Differentially Control CNS Synaptic Function, Plasticity, and Cognition [Cultured Hippocampal Neurons]
SRP229636	Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia: Whole Genome oxidative bisulfite sequencing data [Brain]
SRP230210	Whole genome bisulfite sequencing (WGBS) of Tex15 wt, Tex15 ht, and Tex15 ko male germ cells at postnatal day 2.5 [Germ]
SRP230428	Tet2 negatively regulates memory fidelity [CA1 Hippocampal Tissue]
SRP233665	The role of Vitamin C and TET dioxygenases in genome-wide features of regulatory T cells [WGBS] [Spleen And Lymph Nodes]
SRP234410	Whole Genome Bisulfite Sequencing Facilitates Quantitative Analysis of DNA Methylation status in sperm from 2 month old and 18 month old mice [Sperm]
SRP234989	Transcriptomic and epigenetic disruptions in excitatory neurons in Dnmt3a conditional knockout mouse [Brain (Frontal Cortex)]
SRP237267	Maternal DNMT3A-dependent de novo methylation of the zygotic paternal genome inhibits gene expression in the early embryo [BB androgenetic blasto DNAme, Embryo]
SRP239190	DNMTs Play an Important Role in Maintaining the Pluripotency of Leukemia Inhibitory Factor Dependent Embryonic Stem Cells [ESC]
SRP239280	Structural basis of epigenetic protection of mouse lymphoid progenitor cells by Dnmt1 [Mouse WGBS] [Lin-Bone Marrow Progenitors]
SRP239769	DNA methylome analysis of directly induced oocyte-like cells (DIOLs) [ESC, Fully-grown directly induced oocyte-like, Non-growing directly induced oocyte-like]
SRP242576	Epigenetic changes in Langerhans islets preceding the onset of diabetes [Islet]
SRP242612	Whole Genome Bisulfite Sequencing of CD4+ T cells from mice developmentally exposed to vehicle or TCDD prior to and during influenza infection [CD4+ T cells]
SRP244650	Paradoxical whole genome DNA methylation dynamics of Decitabine in chronic low-dose exposure in mice [Liver, Testes]
SRP246238	Disturbed mitochondrial dynamics in CD8+ TIL reinforce epigenetic programming linked with T cell exhaustion [CD8+ intratumoral T cells (in vivo FACS purified cells)]
SRP246664	Autocrine IL6 activates the STAT3-DNMT axis to silence the TNFa-RIP1 necroptosis pathway to sustain myeloid-derived suppressor cell survival and accumulation [Spleen]
SRP246939	Beta cell-specific CD8+ T cells maintain stem-cell memory-associated epigenetic programs during type 1 diabetes (WGBS) [HAART HIV TN CD8 T cells, Polyclonal Naive CD8 T cell HD, Polyclonal T1D Naive CD8 T cells, Polyclonal TCM CD8 T cells, Polyclonal TEM CD8 T cells, Polyclonal TSCM CD8 T cells, Tetramer+ CD8 T cells, Tetramer+ HAART CD8 T cells, Tetramer+ T1D CD8 T cells]
SRP247347	TET2 promotes anti-tumor immunity by governing G-MDSCs and CD8+ T cell numbers [granulocytic myeloid-derived suppressor cells (G-MDSCs)]
SRP250290	A multivalent signal-transducing model for the DNMT1-mediated maintenance DNA methylation [ESC]
SRP251304	Control of Foxp3 induction and maintenance by sequential histone acetylation and DNA demethylation [WGBS] [In vitro induced wild-type regulatory T cells (ascorbic acid treated), In vitro induced wild-type regulatory T cells (control), Wild-type CD4 effector T cells, Wild-type naive CD4 T cells, Wild-type regulatory T cells]
SRP252412	WGBS and RNA-seq of mouse livers and human Hep3B cells [Liver]
SRP254051	Post-implantation developmental defects induced by mtDNA mutation derive from altered DNA methylome in oocytes [Oocyte]
SRP254510	Mus musculus musculus strain:Bl6 Raw sequence reads [Enterocytes]
SRP254904	DNMT3A haploinsufficiency results in behavioral deficits and global epigenomic dysregulation shared across neurodevelopment disorders [Bisulfite-Seq] [Cortex]
SRP255391	NSD1-deposited H3K36me2 directs de novo methylation in the mouse male germline and counteracts Polycomb-associated silencing [Embryo, Sperm]
SRP257580	Altered microRNA expression links IL6 and TNF-induced inflammaging with myeloid malignancy [miR146aKO_LSK_WGBS] [Bone Marrow]
SRP257737	Role of E2F6 in gene expression and DNA methylation during mouse development [Whole Embryos]
SRP257778	Characterization of metabolic patterns in mouse oocytes during meiotic maturation [MII oocytes]
SRP258361	Transgenerational inheritance of obesity correlates with transmission of epigenetic alterations in the Fto gene [BS-seq] [Sperm]
SRP258472	Neuronal activation modulates enhancer activity of genes for excitatory synaptogenesis through de novo DNA methylation [E17 hippocampus]
SRP261467	Epigenetic and chromatin profiling of wild-type and Dnmt3a-deficient B1 and B2 B cells. (methylation) [B1, B2, proB1, proB2]
SRP261529	An activity-mediated transition in transcription in early postnatal neurons [BS-seq] [Cortex]
SRP265159	IGF2R-initiated Proton Rechanneling Dictates an Anti-inflammatory Property in Macrophages [Peritoneal Macrophages]
SRP265261	Cyclosporin A and FGF signaling support the proliferation/survival of mouse primordial germ cell-like cells in vitro [bis-seq] [E9.5 PGC, ESC]
SRP265512	Temporal evolution of cellular heterogeneity during the progression to advanced, AR-negative prostate cancer [RRBS] [Tumor]
SRP266415	Flanking sequence preference modulates de novo DNA methylation in the mouse genome [ESC]
SRP266608	Mouse preimplantation imprinting [WGBS] [Blastocyst, ESC, Kidney]
SRP267895	Multiomics profiling of young and old quiescent skeletal muscle stem cells [aging WGBS] [Skeletal Muscle Stem Cell]
SRP267967	Characterization of universal features of partially methylated domains across tissues and species [Breast Tumor, Lung]
SRP270999	Hoxa10 is a functional positional memory that governs stem cell function in adult skeletal muscle [Masseter, Tibialis Anterior]
SRP271091	Glucocorticoids sensitive progenitor PDGFRa+ cells switching to white adipocytes cause visceral obese via methylation modification of TEAD1 (Bisultite-seq) [Adipose]
SRP271469	Methylation and gene expression data obtained from Dnmt3b+/- peripheral T-cell lymphomas. [Lymph Node]
SRP271532	Formative pluripotent stem cells show features of epiblast cells poised for gastrulation [MethylC fPSCs P10]
SRP271992	Methylation and gene expression data obtained from Dnmt3b+/+, Dnmt3bD/D and Dnmt3bCI/CI MYC induced T-cell lymphomas (MTCLs). [Lymph Node]
SRP272852	Epigenetic reprogramming of airway macrophages drives polarization and inflammation in muco-obstructive lung disease (WGBS_BL) [Lung]
SRP273163	Atg7-dependent autophagy regulates the naive to primed transition by selective Nanog degradation in mouse embryonic stem cells [WGBS] [ESC]
SRP273620	Whole genome bisulfite sequencing of apoptotic and male-differentiated subpopulations of E13.5 wild-type murine male germ cells [Apoptosis-poised (AP) germ, Male-differentiated (MD) germ]
SRP278195	Whole genome bisulfite sequencing analysis to measure the effect of EHMT2 (G9a, Bat8) on DNA methylation in the mouse embryo at 9.5 dpc [Embryo]
SRP280273	Fetal origin of sex-bias brain aging [Fetal Brain, Placenta]
SRP281855	YY1 safeguard multidimensional epigenetic landscape associated with extended pluripotency [EPS]
SRP282002	Sperm epigenetic alterations contribute to inter- and transgenerational effects of paternal exposure to long-term psychological stress via evading offspring embryonic reprogramming [Embryo, Oocyte, Sperm]
SRP282126	MicroRNA-29 is an essential regulator of non-CG methylation during brain maturation [Bisulfite-seq] [Cortex]
SRP283863	Foxp3 enhancers synergize to maximize regulatory T cell suppressive capacity [Bisulfite-Seq] [FACS sorted regulatory T cells (CD4+GFP+)]
SRP285138	Dnmt1 has global de novo methylation activity and is specifically targeted to transposable elements [E3.5 Blastocyst, E6.5 Epiblast, ESC]
SRP285604	Muscle regeneration controlled by a designated DNA dioxygenase (Methylation-Seq) [Hindlimb Skeletal Muscle]
SRP286191	Genome-wide maps of Dnmt1-dependent DNA methylome in adipocytes [Epididymal Adipose]
SRP286409	H3K27me3 shapes DNA methylome by inhibiting UHRF1-mediated H3 ubiquitination [Bisulfite-seq] [E14, HeLa]
SRP288034	DNA methylomes of murine B and T cells from the BLUEPRINT Epigenome project [CD4+CD62L+ T cells, CD43-B cells]
SRP288067	Epigenomic profiles of 4T1 cell line in primary, metastasis site and circulating cell type in xenograft mouse model [Circulating Tumor, Fat Pad Xenograft, Lung Metastasis, Mammary Gland]
SRP289001	Depletion of H3K36me2 recapitulates epigenomic and phenotypic changes induced by the H3.3K36M oncohistone mutation [Embryo]
SRP289560	Whole-genome bisulfite sequencing analysis of Pten's function in regulating cardiomyocyte differentiation [ES-derived cardiomyocytes]
SRP291181	Transgenerational inheritance of epigenetic signatures at CpG islands in mice [ESC]
SRP291379	Dnmt3a deficiency in the skin [Skin]
SRP292265	Cell type-specific transcriptomic and eipgenome analysis of diabetic cardiomyopathy [Heart]
SRP292587	TET deficiency promotes oncogenesis and DNA damage in B cells by increasing the levels of G-quadruplexes and R-loops [WGBS] [Spleen]
SRP292755	KMT2C Loss Promotes Small Cell Lung Cancer Metastasis through DNMT3A-mediated Epigenetic Reprogramming [Liver, Lung]
SRP292910	The effect of NEIL3 on CA1 DNA methylation [Brain]
SRP294136	Unraveling the functional role of DNA demethylation at specific promoters by targeted steric blockage of DNA methyltansferase with CRISPR/dCas9 [NIH-3T3]
SRP296451	WGBS on prospermatogonia at E18.5 [Prospermatogonia (Oct4-GFP positive cells sorted by FACS)]
SRP297323	Base-editor-mediated multiplexed inactivation of DNA methyltransferases reveals essential roles of miRNAs in mouse gastrulation [Epiblast, Extraembryonic Ectoderm, Whole Embryo]
SRP297921	Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation [II] [Small Intestinal Epithelium Derived Organoids]
SRP299927	Methylomes of macrophage-DC progenitors (MDPs), monocytes, common monocyte progenitors (cMoPs), common dendritic cell progenitors (CDPs), plasmacytoid dendritic cells (pDCs), and cDC CD8a+ as well as cDC CD11b+ dendritic cells [CDPs, MDPs, Monocytes, cDC CD11b+, cDC CD8a+, cMoPs, pDCs]
SRP300044	Genome-wide maps of DNA methylome during oocyte aging and its transgenerational inheritance [Hippocampus, M2 oocyte, Sperm]
SRP300086	PDGFRa+ not CD137+ progenitors control visceral obesity via glucocorticoid mediated TEAD1 methylation state [Adipose Tissue]
SRP300442	Disordered N-Terminal DNMT3A Domain Is Required for Mouse Postnatal Development [Cerebral Cortex, Cortical Neuron Nuclei]
SRP301916	Constitutive loss of DNMT3A causes morbid obesity through misregulation of adipogenesis [Adipose]
SRP302177	Whole genome bisulfite sequencing of E13.0 and E13.5 Tex14 mutant, heterozygote and wild-type murine female germ cells [Germ]
SRP302195	Whole genome bisulfite sequencing of sstr2 knockout mice [Gastric]
SRP302337	ZFP57 dictates allelic expression switch of target imprinted genes [Total Embryo]
SRP305480	5-hydroxymethylcytosine is required for terminal differentiation of Purkinje neurons [Cerebellum]
SRP307526	DNA methylation regulates haematopoietic development [AGM, Bone Marrow, Fetal Liver]
SRP308565	Methylomes of young and aged LT-HSCs [Primary Murine Hematopoietic Stem Cell]
SRP308731	Loss of SETD1B results in the redistribution of genomic H3K4me3 in the oocyte [PBAT] [Germinal Vesicle Oocytes]
SRP309189	Genome-wide methylation analysis of murine innate lymphoid cells [Lymph Node]
SRP309253	In Vitro Reconstitution of the Whole Male Germ-Cell Development from Mouse Pluripotent Stem Cells [PBAT] [Germ cells derived from ESCs]
SRP309373	RNA-seq, ATAC-seq, WGBS, and CUT&RUN of urothelial cells isolated from Naive, Resolved, and Sensitized C3H/HeN mice [urothelial stem cells (USCs)]
SRP309644	DNMT3B supports meso-endoderm differentiation from mouse embryonic stem cells [WGBS] [ES-E14, ES-E14 derived EpiSC, EpiLC-derived ME]
SRP309709	Epigenetic integrity of paternal imprints enhances the developmental potential of androgenetic haploid embryonic stem cells [ESC]
SRP310260	Mouse totipotent stem cells captured and maintained through spliceosomal repression [mESC cultured in SLP medium, mESC cultured in serum/lif medium]
SRP310416	Dnmt3a-Mutant Hematopoietic Stem cells are resistant to inflammatory stress [Bone Marrow]
SRP311975	A cis-acting mechanism mediates trancriptional memory at Polycomb target genes in mammals [WGBS] [C-Myc-Immortalized Mouse Embryonic Fibroblasts]
SRP312013	Maintenance DNA methylation in pre-meiotic germ cells regulates meiotic prophase by facilitating homologous chromosome pairing [Male Germ]
SRP312491	Placenta and fetal brain share a neurodevelopmental disorder DNA methylation profile in a mouse model of prenatal PCB exposure [WGBS] [Brain, Placenta]
SRP312798	Diverse epigenetic mechanisms maintain parental imprints within the embryonic and extraembryonic lineages [ExE (Extraembryonic Ectoderm)]
SRP313361	Whole Genome Bisulfite Sequencing of miR-143 knock-out mice liver
SRP313387	Regnase-1 suppresses TCF-1+ precursor exhausted T cell formation to limit CAR T cell responses against ALL [WGBS] [Regnase-1-deficient CAR T, Wt Car T]
SRP313733	Whole genome bisulfite sequencing of young and old satellite cells [Primary Myoblasts]
SRP314467	Postnatal expansion of the lymph node stromal cell pool towards reticular and CD34+ stromal cell subsets [WGBS] [Gut-Draining Mesenteric Lymph Node, Skin-Draining Mesenteric Lymph Node]
SRP315002	Functional and epigenetic phenotypes of humans and mice with DNMT3A overgrowth syndrome [Whole Bone Marrow]
SRP318894	RNA-seq, WGBS, 5hmC-Seal, and ATAC-seq data about TET proteins and skeletal development (WGBS) [Primary]
SRP319090	Whole genome bisulfite sequencing analysis to examine the effect of the iron chelator deferoxamine on DNA methylation levels in 3T3-L1 pre-adipocyte cells [Preadipocyte Cell Line]
SRP319425	Whole-genome bisulfite sequencing anlaysis of in vitro fertilized mouse hybrid blastocysts [Blastocyst]
SRP321573	Conservation and divergence of DNA methylation patterns and functions in vertebrates [Primary Dermal Fibroblasts, Psoas Muscle]
SRP321876	Genetic variation at mouse and human ribosomal DNA influences associated epigenetic states [Blood, Kidney]
SRP322748	Club cells employ regeneration mechanisms during lung tumorigenesis [Lung]
SRP323244	Tet enzymes are required for mammalian embryonic hematopoiesis [Endothelial, Hematopoietic Stem And Progenitor]
SRP325428	Systematic profiling of DNMT3A variants reveals protein instability mediated by the DCAF8 E3 ubiquitin ligase adaptor [Cell Line, ESC]
SRP327113	DNA methylation changes of heart tissue in mouse with alcoholic cardiomyopathy [Heart]
SRP329327	HypoSUMOylation in embryonic stem cells generates head-and-trunk embryo-like structure [Methyl-seq] [ESC]
SRP329752	Whole genome bisulfite sequencing (WGBS) analysis of murine splenic DC subtypes [Spleen]
SRP329853	Mouse methylome and transcriptome of three brain tissues in aging [Hippocampus, Striatum, Substantia Nigra]
SRP331841	DNA Methylation Status in Mouse Liver Affected by Maternal High-fat, High-sucrose diet [Liver]
SRP336016	Salt induces hepatic inflammatory response through epigenetic modulation of SIRT3 [Bisulfite-seq] [Liver]
SRP336168	Tet2 deficiency altered hematopoietic stem and progenitor cells ageing process [LSK]
SRP336573	Perturbation of TET2 condensation induces genome-wide promiscuous DNA hypomethylation and curtails leukemia cell growth [ESCs (mESCs), Leukemia Cell Line]
SRP336725	Histone H3K36me2 and H3K36me3 form a chromatin platform essential for DNMT3A-dependent DNA methylation in mouse oocytes [Oocyte]
SRP336812	Differential regulation of mouse hippocampal gene expression sex differences by chromosomal content and gonadal sex: Whole Genome OXBS-Seq Data [Hippocampus]
SRP337056	The DNMT1 inhibitor GSK-3484862 mediates global demethylation in murine embryonic stem cells [ESC]
SRP337411	Examining age-dependent DNA methylation patterns and gene expression in the male and female mouse hippocampus [Dorsal Hippocampus]
SRP339235	9sCa: MSL2 is an allelic dosage sensor in mammals [Neural Progenitor]
SRP339236	BlCa: MSL2 is an allelic dosage sensor in mammals [Neural Progenitor]
SRP339237	CaBl: MSL2 is an allelic dosage sensor in mammals [Neural Progenitor]
SRP339793	Somatic Dnmt3a deletion in murine hematopoietic cells [B-cells, CMP, GMP, Lineage negative Kit positive Sca1 positive, MEP, Myeloid, T-cells, Whole Bone Marrow]
SRP340739	Loss of TET reprograms Wnt signaling through impaired demethylation to promote lung cancer development [Lung]
SRP341070	Promoter repression and 3D-restructuring resolves divergent developmental gene expression in TADs [WGBS] [ESC, Limb]
SRP342398	Next Generation Sequencing Facilitates Quantitative Analysis of ApoE-/-/SAHHWT, ApoE-/-/SAHH+/- mice and ApoE-/-/SAHH+/- +Betaine mice [WGBS] [Vascular]
SRP342541	Maternal SMCHD1 controls both imprinted Xist expression and imprinted X chromosome inactivation [Embryo]
SRP342588	Whole genome bisulfite sequencing of 3T3-L1 preadipocytes and adipocytes [Embryo]
SRP342595	Dynamics of DNA hydroxymethylation and methylation during mouse embryonic and germline development [Epiblast]
SRP342917	Rat and mouse imprintomes (allele-specific DNA methylomes) [EPC, Epiblast]
SRP342995	H3K36 Dimethylation Shapes the Epigenetic Interaction Landscape by Directing Repressive Chromatin Modifications in Embryonic Stem Cells [C57BL/6 x 129S4/SvJae F1 embryo-derived ESCs]
SRP348783	Sex-specific epigenetic development in the mouse hypothalamic arcuate nucleus pinpoints human genomic regions associated with body mass index [Glia, Neuron]
SRP349681	The distinct effects of MEK and GSK3 inhibition upon the DNA methylome and transcriptome of mouse embryonic stem cells [ESC]
SRP350023	Vitamin C deficiency causes cell type-specific epigenetic reprogramming and acute tubular necrosis [Kidney]
SRP350997	GLP is critical for oogenesis exhibiting a G9A-independent role in transcriptional repression [Oocyte]
SRP351062	Whole genome DNA methylation profiling of mouse nucleus accumbens Drd2 medium spiny neurons by using two independent library preparation methods [Nucleus Accumbens]
SRP351503	Cell-type specific DNA methylome signatures reveal epigenetic mechanisms for neuronal diversity and neurodevelopmental disorder [Cerebellum, Cortex]
SRP353039	WGBS of control and DAC-treated CT26 cells. [Cell Line]
SRP353283	Cancer stem cells, not bulk tumor cells, determine mechanisms of resistance to SMO inhibitors
SRP354658	Global DNA methylation analysis of cancer-associated fibroblasts reveals extensive epigenetic rewiring linked with RUNX1 upregulation in breast cancer stroma [WGBS] [Breast Tumor, Normal Mammary Fat Pad]
SRP355808	Somatic Dnmt3a deletion in murine hematopoietic cells [B-cells, CMP, GMP, KLS, MEP, Myeloid, T-cells, WBM]
SRP355886	Whole-genome bisulfite sequencing (WGBS) of stressed and nonstressed breast tumor in mice [Breast Tumor]
SRP356163	PU.1-dependent enhancer inhibition separates clonal hematopoiesis from malignant transformation (oxBS-Seq) [Bone Marrow]
SRP357383	DNA methylation landscape and transcriptome of tumor-associated macrophages reveals pathways, transcription factors, and prognostic value relevant for breast cancer patients [methylation] [Bone Marrow, Breast Cancer, Normal Mammary Fat Pad]
SRP359332	Donor T-cell DNMT3a regulates alloreactivity in murine models of hematopoietic stem cell transplantation [WGBS] [Primary]
SRP360183	Whole genome bisulfite sequencing of WT and Dnmt3a KO HSCs following chronic infection [murine Hematpoietic stem cell]
SRP360425	Role of Dppa3 during primordial germ cell development I [primordial germ cell (PGC)]
SRP361168	Suppression of colorectal cancer by ketogenic diet and beta-hydroxybutyrate (Bisulfite Sequencing Dataset) [Colon]
SRP362787	Genome-wide bisulfite sequencing (GWBS) and RNA-seq in hippocampus of Neil1- and Neil2 deficient mice [Hippocampus]
SRP363476	Dynamic antagonism between key repressive pathways maintains the placental epigenome (WGBS) [Trophoblast Stem Cell]
SRP363630	Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet [ESC]
SRP364004	Transcriptional regulation of the thymus master regulator Foxn1 [WGBS] [Lung, Thymus]
SRP366957	Single substitution in H3.3G34 alters DNMT3A recruitment to cause progressive neurodegeneration [WGBS] [Cortex]
SRP367185	Spatial organization of H3K9me2/3-marked heterochromatin is redundantly maintained by either the H3K9 or H3K27 methylation pathway [MethylC-seq] [iMEFs]
SRP367537	Whole-genome bisulfite sequencing of Dnmt1/3a/3b triple knockout (TKO) embryonic stem cells with or without expression of exogenous Dnmt1 before and after cell differentiation [ESC]
SRP367683	TET2 and TET3 loss disrupts small intestine differentiation and homeostasis [Bisulfite-seq] [Small Intestine]
SRP367742	HIV Tat and cocaine interactively alter genome-wide DNA methylation and gene expression and exacerbate learning and memory impairments [Bisulfite-seq] [Brain Hippocampus]
SRP367910	Inflammatory exposure drives permanent impairment of hematopoietic stem cell self-renewal activity and accelerated aging [Lin(-) c-kit(+) sca-1(+) CD150(+) CD48(-) CD34(-)]
SRP368317	Genome-wide methylation analysis of murine CD4+ Th1, Th2, and Th17 cells [Spleen Lymph Node]
SRP370019	Disturbance on DNA methylation and gene expression levels of mouse plasma leukocytes by low-dose ionizing radiation [Plasma Leukocyte]
SRP371705	MethylC-Seq: Intestinal stem cell aging signature reveals a reprogramming strategy to enhance regenerative potential [intestinal stem cell (ISC)]
SRP371845	Raw WGBS reads of mice zygotes [Oocyte, Sperm, Zygotes From The Control, zygotes from the Tet1, zygotes from the Tet2]
SRP372616	Global DNA methylation analysis of mouse totipotent potential stem cells, extended pluripotent stem cells and mouse embryonic stem cells [ESC, Extended Pluripotent Stem Cell, Totipotent Potential Stem Cell]
SRP373182	TRIM28 establishes skeletal stem cell identity and safeguards skeletogenesis (WGBS) [Rib Caritilage]
SRP375715	Role of Dppa3 during primordial germ cell development II [Oocyte]
SRP376172	DNA sequence determines epigenetic bistability at imprinting control regions [WGBS] [ESC]
SRP376633	H3K36 methylation maintains cell identity by regulating opposing lineage programs [Reprogramming Intermediate]
SRP376940	Temporally-Divergent Regulatory Mechanisms Govern Neuronal Diversification and Maturation in the Neocortex [WGBS] [Somatosensory Cortex And Motor Cortex]
SRP377658	Genome-wide assessment of DNA methylation alterations induced by superovulation, sexual immaturity and in vitro follicle growth in mouse blastocysts [Blastocyst]
SRP378380	WGBS data of enhanced addictive bahavior in male offspring [Brain-Nucleus Accumbens]
SRP379742	The intrinsic and extrinsic effects of Tet proteins during gastrulation [Sorted Ctrl1 cells from E8.5 mixed chimeras, Sorted Ctrl2 cells from E8.5 mixed chimeras, Sorted TKO1 cells from E8.5 mixed chimeras, Sorted TKO2 cells from E8.5 mixed chimeras]
SRP381882	In vivo loss of TET2 and TET2 results in aberrant differentiation and homeostasis in the small intestine [Colon Epithelial]
SRP384348	Evidence that direct inhibition of transcription factor binding is the prevailing mode of gene and repeat repression by DNA methylation [WGBS-Seq] [Ebryonic Stem Cell, Embryonic Kidney, Ngn2 neurons]
SRP387245	Differences in DNA methylation of HAMP in blood cells predicts the development of type 2 diabetes [WGBS] [Liver]
SRP388596	Decitabine-induced T cell remodeling facilitates a high antitumor response to PD-1 blockade therapy by promoting the expansion and effector function of CD8+ progenitor exhausted T cells [Spleen]
SRP388748	Transcriptional and epigenetic reprogramming mediated by chronic IL1ß exposure drives self-renewal ability and myeloid priming in TET2 deficient stem and progenitor cells [Bisulfite-Seq] [Bone Marrow]
SRP393350	Whole genome enzymatic methyl-seq of A20 mouse cells using a novel TETact activation of CD4 [A20 B cell lymphoma cell line]
SRP393405	scNMT-seq of the adult NSC lineage - MAB-seq [Ventricular-Subventricular Zone]
SRP393949	CDCA7-associated global aberranDNA hypomethylation translates to localized, tissue-specific transcriptional responses [WGBS] [Spleen]
SRP395725	Tet2 and Tet3 mediated active cytosine hydroxymethylation in Six2 progenitor cells is critical for nephron progenitor differentiation and nephron endowment [Nephron Progenitor]
SRP395892	DNA dioxygenases Tet2/3 control epithelial differentiation (bisulfite-seq) [Hair Matrix Keratinocytes]
SRP396119	NSD1 deposits Histone H3 lysine 36 dimethylation to pattern non-CG DNA methylation in neurons [WGBS in vitro] [Cultured Cortical Neurons]
SRP396130	NSD1 deposits Histone H3 lysine 36 dimethylation to pattern non-CG DNA methylation in neurons [WGBS in vivo] [Cerebral Cortex]
SRP396513	Rockfish: Detection of 5mC DNA Modifications Using Raw Nanopore Signal [ESC, Purified Cardiomyocyte]
SRP397149	Basal cell extrusion primes pluripotent cells for differentiation [Embryo]
SRP397538	Tet2 regulates Sin3a recruitment at active enhancers in embryonic stem cells [ESC]
SRP398423	TET2 lesions enhance the aggressiveness of CEBPA-mutant AML by rebalancing GATA2 expression [WGBS] [AML blasts from bone marrow]
SRP398560	Whole-genome bisulfite sequencing and histone 3.3 ChIP-seq of microdissected developing mouse lens [Lens]
SRP398698	Prenatal exposure to benzo[a]pyrene depletes ovarian reserve and masculinizes embryonic ovarian germ cell transcriptome transgenerationally II [Embryonic Gonad]
SRP398703	Prenatal exposure to benzo[a]pyrene depletes ovarian reserve and masculinizes embryonic ovarian germ cell transcriptome transgenerationally I [Embryonic Gonad]
SRP399252	p16 epimutation modulates the tumor microenvironment and promotes malignancy of Apc-mutant colon cancer [Embryonic Fibroblast]
SRP399723	Zmym2 is essential for methylation of germline genes and active transposons in embryogenesis [WGBS-seq] [Whole Embryo]
SRP400264	WGBS WT J1 ESC at D3 of EpiLC differentiation [ESCs (murine)]
SRP400320	Whole genome bisulfite sequencing (WGBS) and RNA-sequencing of preadipocytes from iWAT [iWAT]
SRP400331	DNA methyltransferase inhibition induces dynamic gene expression changes in lung CD4+ T cells of neonatal mice with E. coli pneumonia [RRBS] [Lung]
SRP401089	Dual gene activating and repressive functions of TET1 in germ layer lineage bifurcation distinguished by genomic context and dependence on 5-methylcytosine oxidation [oxWGBS] [mESC B6129S6F1 Tet1, mESC B6129S6F1 Tet1 CRISPR HDR]
SRP403116	Precision pharmacological reversal of strain-specific diet-induced metabolic syndrome in mice informed by epigenetic and transcriptional regulation [Liver]
SRP404930	LN-stem, tumor stem, tumor terminally differentiated CD8 T cells from human kidney cancer [LN, PBMC, Spleen, TDLN, Tumor]
SRP405758	Comparative analysis of epigenomic evolution in mammals [Liver, Skeletal Muscle]
SRP405928	Optimized bisulfite sequencing reveals the lack of 5-methylcytosine in mammalian mitochondrial DNA [WGBS] [Brain, Breast Cancer, ESC, Embryonic Kidney, Hepatocarcinoma, Lung Adenocarcinoma, Melanoma, Neuroblastoma, Platelet]
SRP407097	Sex Chromosomes and Sex Phenotype Contribute to Biased DNA Methylation in Mouse Liver [Liver]
SRP410496	Whole genome bisulfite sequencing and Infinium Mouse Methylation BeadChip using fresh and fresh-frozen mouse epidermis (WGBS) [Epidermis]
SRP412252	Epigenetic changes in food induced anaphylaxis animal model after immunotherapy. [Lymph Node]
SRP413488	Methylation state of latent and proliferative metastatic tumor cells [Lung]
SRP414189	TET activity propagates transcriptional memory through embryonic dormancy [WGBS] [ESC]
SRP417057	Whole-genome bisulfite sequencing analysis for intestinal budding organoids derived from induced or tissue-derived intestinal stem cells, and for mouse embryonic fibroblasts [Embryo, Intestinal Crypt]
SRP417480	Inducible disruption of Tet genes results in myeloid malignancy, readthrough transcription, and a heterochromatin-to-euchromatin switch [WGBS] [Bone Marrow]
SRP418871	Dynamic DNA methylation turnover at the exit of pluripotency epigenetically primes gene regulatory elements for hematopoietic lineage specification [WGBS] [ESC, EpiLC]
SRP421061	DNA methylation in the mouse cochlea promotes maturation of supporting cells and contributes to the failure of hair cell regeneration [Inner Ear Cochlea]
SRP422554	Predicting age in single cells and low coverage DNA methylation data [scBS] [Blood]
SRP422816	Distinct disease mutations in DNMT3A result in a spectrum of behavioral, epigenetic, and transcriptional disruptions [Cortex]
SRP423445	Ultrafast Bisulfite Sequencing for Efficient and Accurate 5-Methylcytosine Detection in DNA and RNA [ESC, Plasma, Stem Cell]
SRP424820	Durable and efficient gene silencing in vivo by hit-and-run epigenome editing [WGMS] [Liver]
SRP425083	T regulatory cells epigenetic changes in food induced anaphylaxis animal model after immunotherapy. [Spleen]
SRP425335	Epigenetic evolution of the Ly49 gene family [Bisulfite-Seq] [Spleen]
SRP426653	Stem Cell Activity-Coupled Suppression of Endogenous Retrovirus Governs Adult Tissue Regeneration [WGBS] [Skin]
SRP431160	Whole genome bisulfite-seq analysis of control and Dnmt3a conditional knockout (cKO) retinal ganglion cells at 2 days post optic nerve crush [Retina]
SRP431846	Histone methylation mediated by NSD1 is required for the establishment and maintenance of neuronal identities [WGBS] [Somatosensory Cortex]
SRP432324	Macrophage recipient WGBS data: Donors infected with Porphyromonas gingivali (WDPg) or sham-infected (WD) and fed a western diet (WD) [Elicited Macrophages]
SRP433931	Prenatal exposure to benzo[a]pyrene depletes ovarian reserve and masculinizes embryonic ovarian germ cell transcriptome transgenerationally [Bisulfite-Seq] [Embryonic Gonad]
SRP435424	Genome-wide methylated CpG status in WT and IRF8KO microglia [WGBS] [FACS-sorted microglia]
SRP435461	Cell-specific and shared regulatory elements control a multi-gene locus active in mammary and salivary glands [Bisulfite-seq] [Liver, Mammary Gland]
SRP440315	Transcriptomic and methylomic analyses of liver tissue in nonalcoholic steatohepatitis [Bisulfite-Seq] [Liver]
SRP441169	HDAC6 deacetylates IDH1 to regulate the homeostasis of hematopoietic stem/progenitor cells [WGBS-seq] [Bone Marrow]
SRP447137	Single cell methylation, RNA, and ATAC sequencing of brain tissue in inbred mouse strains [Brain]
SRP447781	GEO accession GSE236722 is currently private and is scheduled to be released on Jul 06, 2025. [Cell Line]
SRP450385	Catalytic dependent and independent roles of Tet3 in activation of ectodermal and silencing of mesodermal programs during neuroectoderm specification [Neuroectoderm]
SRP451433	Combinational effect of the ADD domains of DNMT3A and DNMT3L on DNA methylation landscapes in mouse germ cells [WGBS] [Fully Grown Oocyte, Sperm]
SRP454736	Sperm DNA methylation defects in a new mouse model of the 5,10-methylenetetrahydrofolate reductase 677C>T variant and correction with moderate dose folic acid supplementation. [Sperm]
SRP455338	Durable and efficient gene silencing in vivo by hit-and-run epigenome editing [WGMS_invitro_revision] [Liver]
SRP456835	DNMT3A Addback [Bone Marrow]
SRP458075	DNA methylation shapes the Polycomb landscape during the transition from naïve-to-primed pluripotency [ESC]
SRP460843	Whole genome bisulfite sequencing (WGBS) of intestinal organoids from mice with graft-versus-host disease [Intestinal]
SRP461642	Whole genome bisulfite sequencing identifies stage- and subtype-specific DNA methylation signatures in pancreatic cancer [Normal Pancreatic Ductal Mouse Organoid, Normal Pancreatic Ductal Patient-Derived Organoid, PanIN mouse organoid, Pancreatic Ductal Adenocarcinoma Mouse Organoid, Pancreatic Ductal Adenocarcinoma Patient-Derived Organoid]
SRP462875	Mus musculus Genome sequencing and assembly [Liver]
SRP462989	Spatio-temporal X-linked gene reactivation in the mouse germline reveals site-specific retention of epigenetic silencing [WGBS] [Embryo]
SRP463129	Genome-wide DNA methylation pattern changes in ESC, and EPSC after treated with T09 [EPSC, EPSC with T09, ESC, NrESC]
SRP464133	Increased global DNA methylation disrupts skeletal muscle homeostasis, promotes age-related decline in muscle function, and reduces muscle plasticity [Skeletal Muscle Iibialis Anterior]
SRP466337	Astrocyte-produced HB-EGF limits autoimmune CNS pathology [WGBS] [Brain And Spinal Cord]
SRP469813	Whole Genome Bisulphite Sequencing of undifferentiated and differentiated NIH3T3L1 [Fibroblast]
SRP469968	FTDC1/2, oocyte-specific cofactors of DNMT1 required for epigenetic regulation and embryonic development (Bisulfite-Seq) [Blastula, Four, Oocyte]
SRP471571	Histone methyltransferase SETDB1 silenced SINE B2 retrotransposons and maintained mitotic cell cycle of neural progenitor cells (WGBS) [Neural Progenitor Cells From Ganglionic Eminence]
SRP472167	FoxA1/2-dependent epigenomic reprogramming drives lineage switching in lung adenocarcinoma [Bisulfite-Seq] [Lung, Lung Tumors]
SRP473050	Source cell-type epigenetic memory persists in induced pluripotent cells but is lost in subsequently derived germline cells [Embryonic Fibroblasts, Inner Cell Mass, Primordial Germ, Primordial Germ Cell Like, Spermatogonial Stem Cell, Tail Tip Fibroblasts]
SRP473623	Mus musculus strain:C57Bl/6J Raw sequence reads [Placenta, Primordial Germ]
SRP474397	De novo Assembly and Delivery of Synthetic Megabase-Scale Human DNA into Mouse Early Embryos [Early Embryo]
SRP474495	Landscape of TFs binding in mouse early embryos [Bisulfite-seq] [Embryo]
SRP474956	Transcriptomic and epigenomic profiling of Tet TKO neural stem cells to study NSC specification and multipotency [ESC, Neural Stem Cell]
SRP475142	DNA methylation memory of acinar-ductal transition state altering Kras-downstream Pi3k and Rho GTPase signaling [Pancreas]
SRP476050	Cohesin trajectories shape the epigenetic and transcriptional landscape of clustered Protocadherin genes for single neuron identities [Olfactory Epithilium]
SRP477968	Extraembryonic gut endoderm cells undergo programmed cell death elimination during development (WGBS) [Extraembryonic endoderm (distal), Extraembryonic endoderm (proximal), Hindgut Endoderm, Midgut Endoderm, Yolk Sac Endoderm]
SRP478001	Global epigenetic stability of liver-resident invariant natural killer T cells in response to cues capable of inducing transcriptional re-programming [Liver]
SRP480077	Remodeling the step-wise mouse placental development by using totipotent blastomere-like stem cells [WGBS] [mTELCs induced from mTBLCs, mTELSC cultured in TX medium, mTELSC-TO cultured in TO medium]
SRP482520	OGT prevents DNA demethylation and suppresses the expression of transposable elements in heterochromatin by restraining TET activity genome-wide (WGBS) [ESC]
SRP484966	Antisense transcription can induce expression memory via stable promoter repression [XX ESCs]
SRP486307	An unbiased genome-wide screen reveals that mouse metastable epialleles are extremely rare [Kidney, Liver]
SRP487504	Sex-Specific DNA Methylation and Gene Expression Changes in Mouse Placentas After Early Preimplantation Alcohol Exposure[Methyl-Seq] [Placenta]
SRP487827	Endocrine islet beta-cell subtypes with differential function are derived from biochemically distinct embryonic endocrine islet progenitors that are regulated by maternal nutrients [endocrine islets postnatal day-2 female mice, endocrine islets postnatal day-2 male mice, endocrine islets postnatal day-60 female mice, endocrine islets postnatal day-60 male mice]
SRP490016	Methylation status of CD4+ and CD11b+ cells from Dnmt3a+/+ or Dnmt3aR878/+ mice [Spleen]
SRP491334	CxxC-finger protein 1 regulates Treg fragility associated with H3K4me3 breadth [Treg]
SRP494931	RNAseq, ATAC-seq and WGBS of ICM of blastocysts of mus musculus [Embryo]
SRP496661	Employing multi-omics analyses to understand changes during kidney development in perinatal Interleukin-6 animal model [Kidney]
SRP497496	Increased global DNA methylation by Dnmt3a disrupts skeletal muscle homeostasis, promotes age-related muscle atrophy, and reduces muscle metabolic elasticity [Skeletal Muscle Gastrocnemius]
SRP497502	The chromatin accessibility landscape of mouse oocytes during configuration transition [BS-seq] [Oocyte]
SRP498773	GEO accession GSE262843 is currently private and is scheduled to be released on Jul 01, 2025. [Lymph Node, Tumor]
SRP500539	Maternal obesity induces the meiotic defects and epigenetic alterations during fetal oocyte development [BiSulfite-seq] [Ovary]
SRP501862	Conserved epigenetic hallmarks of T-cell aging during immunity and malignancy [Blood]
SRP503857	Mutant IDH1 inhibition induces reverse transcriptase and dsDNA sensing to activate tumor immunity [mouse WGBS] [Cholangiocarcinoma, Liver]
SRP505989	Transgenerational inheritance of diabetes susceptibility in male offspring with maternal hyperandrogenism [WGBS] [Sperm]
SRP506266	Novel enzyme-based reduced representation method for DNA methylation profiling with low inputs [Tconv cells (CD4+Foxp3YFP-), Tconvcells(CD4+Foxp3YFP-), Treg cells (CD4+CD25+Foxp3-YFP+), Tregcells(CD4+CD25+Foxp3-YFP+)]
SRP511326	CXXC5 stabilizes DNA methylation patterns in mouse embryonic stem cells [Bisulfite-Seq] [ESC]
SRP511364	Maternal loss-of-function of Nlrp2 results in failure of epigenetic reprogramming in mouse oocytes [Ovary]
SRP512476	The role of the TET-dependent DNA demethylation pathway in photoreceptor development and pathology [Retina]
SRP521262	Whole genome bisulfite sequencing of mice treated by mitochondrial transplantation [Brain, Muscle]
SRP521804	Dnmt3a Controls Hematopoietic Stem Cells via DNA Methylation-Independent Regulation of Telomeres [BM, KSL]
SRP522281	Early Moderate Prenatal Alcohol Exposure and Maternal Diet Impact Offspring DNA Methylation Across Species [Brain, Liver]
SRP525939	Non-CG DNA methylation and MeCP2 stabilize repeated tuning of long genes that distinguish closely related neuron types [WGBS] [Cortex]
SRP526206	Tet3 regulates terminal cell differentiation at the metabolic level [E18.5 isolated villi from intestinal epithelium]
SRP526448	Epigenetic regulators of clonal hematopoiesis control CD8 T cell stemness during immunotherapy [Bisulfite-Seq] [Spleen]
SRP531904	The DNA demethylase TET1 modifies the impact of maternal folic acid status on embryonic brain development [Embryonic Brain]
SRP534659	Erosion of somatic tissue identity with loss of the X-linked intellectual disability factor KDM5C [ESC, Extended Epiblast-Like]
SRP540228	The spatial zonation of the placental vasculature is specified by epigenetic mechanisms [WGBS] [Placenta]
SRP540934	Accumulation of epigenetic noise in the corneal epithelium during aging [Cornea]
SRP544973	DNMT3A-dependent DNA methylation shapes the endothelial enhancer landscape [WGBS] [Lung]
SRP545322	DNMT3A-dependent DNA methylation shapes the endothelial enhancer landscape [WGBS II] [Lung]
SRP550944	Whole genome bisulfite sequencing of nicotine-exposed sperm reveals differences in global DNA methylation levels, which would partially reverse following cessation [Sperm]
SRP551216	Transcriptome and DNA methylome in oocytes exposed to gestational diabetes [Ovary]
SRP552104	Comparision of Differential methylation between Control and mutant Dnmt3a [KSL]
SRP552665	Ataxia-telangiectasia mutated kinase disruption enhances the efficacy of radiation therapy in spatially-directed diffuse midline gliomas [Brain]
SRP555757	Developmental exposure to air pollution particulates increases asthma severity, alters the RNA transcriptome, and DNA methylation in female adult progeny [WGMS] [Lung (RML)]
SRP560126	Active DNA demethylation is upstream of rod photoreceptor fate determination and required for retinal development [Bisulfite-Seq] [Whole Retina]
SRP564359	PKM2 mediated mitochondrial reprogramming supports enhanced effector functions in CD8 T cells increasing the anti-tumor efficacy of anti-PD1 therapy [WGBS] [C57BL/6J OT1 mice]
SRP567649	Direct sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution unravels their distinct roles in Alzheimer's disease [BS-Seq mESC] [SRX27866901, SRX27866902]
SRP567652	Direct sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution unravels their distinct roles in Alzheimer's disease [BS-Seq] [SRX27867421, SRX27867422, SRX27867423, SRX27867424, SRX27867425, SRX27867426, SRX27867427, SRX27867428, SRX27867429, SRX27867430, SRX27867431, SRX27867432, SRX27867433, SRX27867434, SRX27867435, SRX27867436]
SRP568175	DAXX is required for spermatogenesis and governs the silencing of LINE1 during meiosis in male [Testis]
SRP570719	Chronic morphine treatment leads to a global DNA hypomethylation via active and passive demethylation mechanisms in mESCs [ESC]
SRP571561	Hypercapnia induces long-term DNA methylation changes in skeletal muscle [Skeletal Muscle]
SRP582128	Maternal Vitamin C Deficiency and Genetic Risk Factors Contribute to Congenital Malformations through Dysregulation of DNA Methylation. [WGBS E11.5] [E11.5 brain]
SRP582251	Maternal Vitamin C Deficiency and Genetic Risk Factors Contribute to Congenital Malformations through Dysregulation of DNA Methylation. [WGBS E8.5] [E8.5 headfold]
SRP590085	NAD+-dependent Sirt6 is a key regulator involved in telomere shortening of in vitro-cultured preimplantation embryos [Bisulfite-Seq] [Muscle tissue and Connective]
SRP590495	mRNA-Engineered CRISPR-Cas Epigenetic Editors Enable Durable and Efficient Gene Silencing in Vivo [WGBS] [Hepa1-6, Liver]

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SRX29083854
SRX29083855
SRX29083856
SRX29083857
SRX29083858
SRX29083859
SRX29083860
SRX29083861
SRX29083862
SRX29083863
SRX29083864
SRX29083865
SRX29083866
SRX29083867
SRX29083868
SRX29083869
SRX29083870
SRX29083871
SRX29083872
SRX29083873
SRX29083874
SRX29083875
SRX29083876
SRX29083877
SRX29083878
SRX29083879
SRX29083880
SRX29083881
SRX29083882
SRX29083883
SRX29083884
SRX29083885
SRX29083886
SRX29083887
SRX29083888
SRX29083889
SRX29083890
SRX29083891
SRX29083892
SRX29083893
SRX29083894
SRX29083895
SRX29083896
SRX29083897
*experiment*
All	*views*	AMR	HMR	CpG methylation	PMD	CpG reads

List subtracks: only selected/visible all ()

	experiment^↓1	views^↓2	Track Name^↓3
hide	SRX29083832	HMR	Liver / SRX29083832 (HMR)	Schema
hide	SRX29083832	AMR	Liver / SRX29083832 (AMR)	Schema
hide Configure	SRX29083832	CpG methylation	Liver / SRX29083832 (CpG methylation)	Schema
hide	SRX29083832	PMD	Liver / SRX29083832 (PMD)	Schema
hide Configure	SRX29083832	CpG reads	Liver / SRX29083832 (CpG reads)	Schema
hide	SRX29083833	AMR	Liver / SRX29083833 (AMR)	Schema
hide	SRX29083833	HMR	Liver / SRX29083833 (HMR)	Schema
hide Configure	SRX29083833	CpG methylation	Liver / SRX29083833 (CpG methylation)	Schema
hide	SRX29083833	PMD	Liver / SRX29083833 (PMD)	Schema
hide Configure	SRX29083833	CpG reads	Liver / SRX29083833 (CpG reads)	Schema
hide	SRX29083834	AMR	Liver / SRX29083834 (AMR)	Schema
hide	SRX29083834	HMR	Liver / SRX29083834 (HMR)	Schema
hide Configure	SRX29083834	CpG methylation	Liver / SRX29083834 (CpG methylation)	Schema
hide	SRX29083834	PMD	Liver / SRX29083834 (PMD)	Schema
hide Configure	SRX29083834	CpG reads	Liver / SRX29083834 (CpG reads)	Schema
hide	SRX29083835	AMR	Liver / SRX29083835 (AMR)	Schema
hide	SRX29083835	HMR	Liver / SRX29083835 (HMR)	Schema
hide Configure	SRX29083835	CpG methylation	Liver / SRX29083835 (CpG methylation)	Schema
hide	SRX29083835	PMD	Liver / SRX29083835 (PMD)	Schema
hide Configure	SRX29083835	CpG reads	Liver / SRX29083835 (CpG reads)	Schema
hide	SRX29083836	AMR	Liver / SRX29083836 (AMR)	Schema
hide	SRX29083836	HMR	Liver / SRX29083836 (HMR)	Schema
hide Configure	SRX29083836	CpG methylation	Liver / SRX29083836 (CpG methylation)	Schema
hide	SRX29083836	PMD	Liver / SRX29083836 (PMD)	Schema
hide Configure	SRX29083836	CpG reads	Liver / SRX29083836 (CpG reads)	Schema
hide	SRX29083837	AMR	Liver / SRX29083837 (AMR)	Schema
hide	SRX29083837	HMR	Liver / SRX29083837 (HMR)	Schema
hide Configure	SRX29083837	CpG methylation	Liver / SRX29083837 (CpG methylation)	Schema
hide	SRX29083837	PMD	Liver / SRX29083837 (PMD)	Schema
hide Configure	SRX29083837	CpG reads	Liver / SRX29083837 (CpG reads)	Schema
hide	SRX29083838	AMR	Liver / SRX29083838 (AMR)	Schema
hide	SRX29083838	HMR	Liver / SRX29083838 (HMR)	Schema
hide Configure	SRX29083838	CpG methylation	Liver / SRX29083838 (CpG methylation)	Schema
hide	SRX29083838	PMD	Liver / SRX29083838 (PMD)	Schema
hide Configure	SRX29083838	CpG reads	Liver / SRX29083838 (CpG reads)	Schema
hide	SRX29083839	AMR	Liver / SRX29083839 (AMR)	Schema
hide	SRX29083839	HMR	Liver / SRX29083839 (HMR)	Schema
hide Configure	SRX29083839	CpG methylation	Liver / SRX29083839 (CpG methylation)	Schema
hide	SRX29083839	PMD	Liver / SRX29083839 (PMD)	Schema
hide Configure	SRX29083839	CpG reads	Liver / SRX29083839 (CpG reads)	Schema
hide	SRX29083840	AMR	Liver / SRX29083840 (AMR)	Schema
hide	SRX29083840	HMR	Liver / SRX29083840 (HMR)	Schema
hide Configure	SRX29083840	CpG methylation	Liver / SRX29083840 (CpG methylation)	Schema
hide	SRX29083840	PMD	Liver / SRX29083840 (PMD)	Schema
hide Configure	SRX29083840	CpG reads	Liver / SRX29083840 (CpG reads)	Schema
hide	SRX29083841	AMR	Liver / SRX29083841 (AMR)	Schema
hide	SRX29083841	HMR	Liver / SRX29083841 (HMR)	Schema
hide Configure	SRX29083841	CpG methylation	Liver / SRX29083841 (CpG methylation)	Schema
hide	SRX29083841	PMD	Liver / SRX29083841 (PMD)	Schema
hide Configure	SRX29083841	CpG reads	Liver / SRX29083841 (CpG reads)	Schema
hide	SRX29083842	AMR	Liver / SRX29083842 (AMR)	Schema
hide	SRX29083842	HMR	Liver / SRX29083842 (HMR)	Schema
hide Configure	SRX29083842	CpG methylation	Liver / SRX29083842 (CpG methylation)	Schema
hide	SRX29083842	PMD	Liver / SRX29083842 (PMD)	Schema
hide Configure	SRX29083842	CpG reads	Liver / SRX29083842 (CpG reads)	Schema
hide	SRX29083843	AMR	Liver / SRX29083843 (AMR)	Schema
hide	SRX29083843	HMR	Liver / SRX29083843 (HMR)	Schema
hide Configure	SRX29083843	CpG methylation	Liver / SRX29083843 (CpG methylation)	Schema
hide	SRX29083843	PMD	Liver / SRX29083843 (PMD)	Schema
hide Configure	SRX29083843	CpG reads	Liver / SRX29083843 (CpG reads)	Schema
hide	SRX29083844	AMR	Liver / SRX29083844 (AMR)	Schema
hide	SRX29083844	HMR	Liver / SRX29083844 (HMR)	Schema
hide Configure	SRX29083844	CpG methylation	Liver / SRX29083844 (CpG methylation)	Schema
hide	SRX29083844	PMD	Liver / SRX29083844 (PMD)	Schema
hide Configure	SRX29083844	CpG reads	Liver / SRX29083844 (CpG reads)	Schema
hide	SRX29083845	AMR	Liver / SRX29083845 (AMR)	Schema
hide	SRX29083845	HMR	Liver / SRX29083845 (HMR)	Schema
hide Configure	SRX29083845	CpG methylation	Liver / SRX29083845 (CpG methylation)	Schema
hide	SRX29083845	PMD	Liver / SRX29083845 (PMD)	Schema
hide Configure	SRX29083845	CpG reads	Liver / SRX29083845 (CpG reads)	Schema
hide	SRX29083846	AMR	Liver / SRX29083846 (AMR)	Schema
hide	SRX29083846	HMR	Liver / SRX29083846 (HMR)	Schema
hide Configure	SRX29083846	CpG methylation	Liver / SRX29083846 (CpG methylation)	Schema
hide	SRX29083846	PMD	Liver / SRX29083846 (PMD)	Schema
hide Configure	SRX29083846	CpG reads	Liver / SRX29083846 (CpG reads)	Schema
hide	SRX29083847	AMR	Liver / SRX29083847 (AMR)	Schema
hide	SRX29083847	HMR	Liver / SRX29083847 (HMR)	Schema
hide Configure	SRX29083847	CpG methylation	Liver / SRX29083847 (CpG methylation)	Schema
hide	SRX29083847	PMD	Liver / SRX29083847 (PMD)	Schema
hide Configure	SRX29083847	CpG reads	Liver / SRX29083847 (CpG reads)	Schema
hide	SRX29083848	AMR	Liver / SRX29083848 (AMR)	Schema
hide	SRX29083848	HMR	Liver / SRX29083848 (HMR)	Schema
hide	SRX29083848	PMD	Liver / SRX29083848 (PMD)	Schema
hide Configure	SRX29083848	CpG methylation	Liver / SRX29083848 (CpG methylation)	Schema
hide Configure	SRX29083848	CpG reads	Liver / SRX29083848 (CpG reads)	Schema
hide	SRX29083849	AMR	Liver / SRX29083849 (AMR)	Schema
hide	SRX29083849	HMR	Liver / SRX29083849 (HMR)	Schema
hide Configure	SRX29083849	CpG methylation	Liver / SRX29083849 (CpG methylation)	Schema
hide	SRX29083849	PMD	Liver / SRX29083849 (PMD)	Schema
hide Configure	SRX29083849	CpG reads	Liver / SRX29083849 (CpG reads)	Schema
hide	SRX29083850	AMR	Liver / SRX29083850 (AMR)	Schema
hide	SRX29083850	HMR	Liver / SRX29083850 (HMR)	Schema
hide Configure	SRX29083850	CpG methylation	Liver / SRX29083850 (CpG methylation)	Schema
hide	SRX29083850	PMD	Liver / SRX29083850 (PMD)	Schema
hide Configure	SRX29083850	CpG reads	Liver / SRX29083850 (CpG reads)	Schema
hide	SRX29083851	HMR	Liver / SRX29083851 (HMR)	Schema
hide	SRX29083851	AMR	Liver / SRX29083851 (AMR)	Schema
hide Configure	SRX29083851	CpG methylation	Liver / SRX29083851 (CpG methylation)	Schema
hide	SRX29083851	PMD	Liver / SRX29083851 (PMD)	Schema
hide Configure	SRX29083851	CpG reads	Liver / SRX29083851 (CpG reads)	Schema
hide	SRX29083852	AMR	Liver / SRX29083852 (AMR)	Schema
hide	SRX29083852	HMR	Liver / SRX29083852 (HMR)	Schema
hide Configure	SRX29083852	CpG methylation	Liver / SRX29083852 (CpG methylation)	Schema
hide	SRX29083852	PMD	Liver / SRX29083852 (PMD)	Schema
hide Configure	SRX29083852	CpG reads	Liver / SRX29083852 (CpG reads)	Schema
hide	SRX29083853	AMR	Liver / SRX29083853 (AMR)	Schema
hide	SRX29083853	HMR	Liver / SRX29083853 (HMR)	Schema
hide Configure	SRX29083853	CpG methylation	Liver / SRX29083853 (CpG methylation)	Schema
hide	SRX29083853	PMD	Liver / SRX29083853 (PMD)	Schema
hide Configure	SRX29083853	CpG reads	Liver / SRX29083853 (CpG reads)	Schema
hide	SRX29083854	AMR	Liver / SRX29083854 (AMR)	Schema
hide	SRX29083854	HMR	Liver / SRX29083854 (HMR)	Schema
hide Configure	SRX29083854	CpG methylation	Liver / SRX29083854 (CpG methylation)	Schema
hide	SRX29083854	PMD	Liver / SRX29083854 (PMD)	Schema
hide Configure	SRX29083854	CpG reads	Liver / SRX29083854 (CpG reads)	Schema
hide	SRX29083855	AMR	Liver / SRX29083855 (AMR)	Schema
hide	SRX29083855	HMR	Liver / SRX29083855 (HMR)	Schema
hide Configure	SRX29083855	CpG methylation	Liver / SRX29083855 (CpG methylation)	Schema
hide	SRX29083855	PMD	Liver / SRX29083855 (PMD)	Schema
hide Configure	SRX29083855	CpG reads	Liver / SRX29083855 (CpG reads)	Schema
hide	SRX29083856	AMR	Liver / SRX29083856 (AMR)	Schema
hide	SRX29083856	HMR	Liver / SRX29083856 (HMR)	Schema
hide Configure	SRX29083856	CpG methylation	Liver / SRX29083856 (CpG methylation)	Schema
hide	SRX29083856	PMD	Liver / SRX29083856 (PMD)	Schema
hide Configure	SRX29083856	CpG reads	Liver / SRX29083856 (CpG reads)	Schema
hide	SRX29083857	AMR	Liver / SRX29083857 (AMR)	Schema
hide	SRX29083857	HMR	Liver / SRX29083857 (HMR)	Schema
hide Configure	SRX29083857	CpG methylation	Liver / SRX29083857 (CpG methylation)	Schema
hide	SRX29083857	PMD	Liver / SRX29083857 (PMD)	Schema
hide Configure	SRX29083857	CpG reads	Liver / SRX29083857 (CpG reads)	Schema
hide	SRX29083858	AMR	Liver / SRX29083858 (AMR)	Schema
hide	SRX29083858	HMR	Liver / SRX29083858 (HMR)	Schema
hide Configure	SRX29083858	CpG methylation	Liver / SRX29083858 (CpG methylation)	Schema
hide	SRX29083858	PMD	Liver / SRX29083858 (PMD)	Schema
hide Configure	SRX29083858	CpG reads	Liver / SRX29083858 (CpG reads)	Schema
hide	SRX29083859	AMR	Liver / SRX29083859 (AMR)	Schema
hide	SRX29083859	HMR	Liver / SRX29083859 (HMR)	Schema
hide Configure	SRX29083859	CpG methylation	Liver / SRX29083859 (CpG methylation)	Schema
hide	SRX29083859	PMD	Liver / SRX29083859 (PMD)	Schema
hide Configure	SRX29083859	CpG reads	Liver / SRX29083859 (CpG reads)	Schema
hide	SRX29083860	AMR	Liver / SRX29083860 (AMR)	Schema
hide	SRX29083860	HMR	Liver / SRX29083860 (HMR)	Schema
hide Configure	SRX29083860	CpG methylation	Liver / SRX29083860 (CpG methylation)	Schema
hide	SRX29083860	PMD	Liver / SRX29083860 (PMD)	Schema
hide Configure	SRX29083860	CpG reads	Liver / SRX29083860 (CpG reads)	Schema
hide	SRX29083861	AMR	Liver / SRX29083861 (AMR)	Schema
hide	SRX29083861	HMR	Liver / SRX29083861 (HMR)	Schema
hide Configure	SRX29083861	CpG methylation	Liver / SRX29083861 (CpG methylation)	Schema
hide	SRX29083861	PMD	Liver / SRX29083861 (PMD)	Schema
hide Configure	SRX29083861	CpG reads	Liver / SRX29083861 (CpG reads)	Schema
hide	SRX29083862	AMR	Liver / SRX29083862 (AMR)	Schema
hide	SRX29083862	HMR	Liver / SRX29083862 (HMR)	Schema
hide Configure	SRX29083862	CpG methylation	Liver / SRX29083862 (CpG methylation)	Schema
hide	SRX29083862	PMD	Liver / SRX29083862 (PMD)	Schema
hide Configure	SRX29083862	CpG reads	Liver / SRX29083862 (CpG reads)	Schema
hide	SRX29083863	AMR	Liver / SRX29083863 (AMR)	Schema
hide	SRX29083863	HMR	Liver / SRX29083863 (HMR)	Schema
hide Configure	SRX29083863	CpG methylation	Liver / SRX29083863 (CpG methylation)	Schema
hide	SRX29083863	PMD	Liver / SRX29083863 (PMD)	Schema
hide Configure	SRX29083863	CpG reads	Liver / SRX29083863 (CpG reads)	Schema
hide	SRX29083864	AMR	Hepa1-6 / SRX29083864 (AMR)	Schema
hide Configure	SRX29083864	CpG methylation	Hepa1-6 / SRX29083864 (CpG methylation)	Schema
hide	SRX29083864	PMD	Hepa1-6 / SRX29083864 (PMD)	Schema
hide	SRX29083866	HMR	Liver / SRX29083866 (HMR)	Schema
hide Configure	SRX29083864	CpG reads	Hepa1-6 / SRX29083864 (CpG reads)	Schema
hide	SRX29083865	AMR	Hepa1-6 / SRX29083865 (AMR)	Schema
hide Configure	SRX29083865	CpG methylation	Hepa1-6 / SRX29083865 (CpG methylation)	Schema
hide	SRX29083865	PMD	Hepa1-6 / SRX29083865 (PMD)	Schema
hide Configure	SRX29083865	CpG reads	Hepa1-6 / SRX29083865 (CpG reads)	Schema
hide	SRX29083867	HMR	Liver / SRX29083867 (HMR)	Schema
hide	SRX29083866	AMR	Liver / SRX29083866 (AMR)	Schema
hide	SRX29083868	HMR	Liver / SRX29083868 (HMR)	Schema
hide Configure	SRX29083866	CpG methylation	Liver / SRX29083866 (CpG methylation)	Schema
hide	SRX29083866	PMD	Liver / SRX29083866 (PMD)	Schema
hide Configure	SRX29083866	CpG reads	Liver / SRX29083866 (CpG reads)	Schema
hide	SRX29083867	AMR	Liver / SRX29083867 (AMR)	Schema
hide	SRX29083869	HMR	Liver / SRX29083869 (HMR)	Schema
hide	SRX29083867	PMD	Liver / SRX29083867 (PMD)	Schema
hide Configure	SRX29083867	CpG methylation	Liver / SRX29083867 (CpG methylation)	Schema
hide Configure	SRX29083867	CpG reads	Liver / SRX29083867 (CpG reads)	Schema
hide	SRX29083868	AMR	Liver / SRX29083868 (AMR)	Schema
hide	SRX29083870	HMR	Liver / SRX29083870 (HMR)	Schema
hide Configure	SRX29083868	CpG methylation	Liver / SRX29083868 (CpG methylation)	Schema
hide	SRX29083868	PMD	Liver / SRX29083868 (PMD)	Schema
hide Configure	SRX29083868	CpG reads	Liver / SRX29083868 (CpG reads)	Schema
hide	SRX29083869	AMR	Liver / SRX29083869 (AMR)	Schema
hide	SRX29083871	HMR	Liver / SRX29083871 (HMR)	Schema
hide Configure	SRX29083869	CpG methylation	Liver / SRX29083869 (CpG methylation)	Schema
hide	SRX29083869	PMD	Liver / SRX29083869 (PMD)	Schema
hide Configure	SRX29083869	CpG reads	Liver / SRX29083869 (CpG reads)	Schema
hide	SRX29083872	HMR	Liver / SRX29083872 (HMR)	Schema
hide	SRX29083870	AMR	Liver / SRX29083870 (AMR)	Schema
hide Configure	SRX29083870	CpG methylation	Liver / SRX29083870 (CpG methylation)	Schema
hide	SRX29083870	PMD	Liver / SRX29083870 (PMD)	Schema
hide Configure	SRX29083870	CpG reads	Liver / SRX29083870 (CpG reads)	Schema
hide	SRX29083871	AMR	Liver / SRX29083871 (AMR)	Schema
hide	SRX29083873	HMR	Liver / SRX29083873 (HMR)	Schema
hide Configure	SRX29083871	CpG methylation	Liver / SRX29083871 (CpG methylation)	Schema
hide	SRX29083871	PMD	Liver / SRX29083871 (PMD)	Schema
hide Configure	SRX29083871	CpG reads	Liver / SRX29083871 (CpG reads)	Schema
hide	SRX29083872	AMR	Liver / SRX29083872 (AMR)	Schema
hide	SRX29083874	HMR	Liver / SRX29083874 (HMR)	Schema
hide Configure	SRX29083872	CpG methylation	Liver / SRX29083872 (CpG methylation)	Schema
hide	SRX29083872	PMD	Liver / SRX29083872 (PMD)	Schema
hide Configure	SRX29083872	CpG reads	Liver / SRX29083872 (CpG reads)	Schema
hide	SRX29083873	AMR	Liver / SRX29083873 (AMR)	Schema
hide	SRX29083875	HMR	Liver / SRX29083875 (HMR)	Schema
hide Configure	SRX29083873	CpG methylation	Liver / SRX29083873 (CpG methylation)	Schema
hide	SRX29083873	PMD	Liver / SRX29083873 (PMD)	Schema
hide Configure	SRX29083873	CpG reads	Liver / SRX29083873 (CpG reads)	Schema
hide	SRX29083874	AMR	Liver / SRX29083874 (AMR)	Schema
hide	SRX29083876	HMR	Liver / SRX29083876 (HMR)	Schema
hide Configure	SRX29083874	CpG methylation	Liver / SRX29083874 (CpG methylation)	Schema
hide	SRX29083874	PMD	Liver / SRX29083874 (PMD)	Schema
hide Configure	SRX29083874	CpG reads	Liver / SRX29083874 (CpG reads)	Schema
hide	SRX29083875	AMR	Liver / SRX29083875 (AMR)	Schema
hide	SRX29083877	HMR	Liver / SRX29083877 (HMR)	Schema
hide Configure	SRX29083875	CpG methylation	Liver / SRX29083875 (CpG methylation)	Schema
hide	SRX29083875	PMD	Liver / SRX29083875 (PMD)	Schema
hide Configure	SRX29083875	CpG reads	Liver / SRX29083875 (CpG reads)	Schema
hide	SRX29083876	AMR	Liver / SRX29083876 (AMR)	Schema
hide	SRX29083878	HMR	Liver / SRX29083878 (HMR)	Schema
hide Configure	SRX29083876	CpG methylation	Liver / SRX29083876 (CpG methylation)	Schema
hide	SRX29083876	PMD	Liver / SRX29083876 (PMD)	Schema
hide Configure	SRX29083876	CpG reads	Liver / SRX29083876 (CpG reads)	Schema
hide	SRX29083877	AMR	Liver / SRX29083877 (AMR)	Schema
hide	SRX29083879	HMR	Liver / SRX29083879 (HMR)	Schema
hide Configure	SRX29083877	CpG methylation	Liver / SRX29083877 (CpG methylation)	Schema
hide	SRX29083877	PMD	Liver / SRX29083877 (PMD)	Schema
hide Configure	SRX29083877	CpG reads	Liver / SRX29083877 (CpG reads)	Schema
hide	SRX29083878	AMR	Liver / SRX29083878 (AMR)	Schema
hide	SRX29083880	HMR	Liver / SRX29083880 (HMR)	Schema
hide Configure	SRX29083878	CpG methylation	Liver / SRX29083878 (CpG methylation)	Schema
hide	SRX29083878	PMD	Liver / SRX29083878 (PMD)	Schema
hide Configure	SRX29083878	CpG reads	Liver / SRX29083878 (CpG reads)	Schema
hide	SRX29083879	AMR	Liver / SRX29083879 (AMR)	Schema
hide	SRX29083881	HMR	Liver / SRX29083881 (HMR)	Schema
hide Configure	SRX29083879	CpG methylation	Liver / SRX29083879 (CpG methylation)	Schema
hide	SRX29083879	PMD	Liver / SRX29083879 (PMD)	Schema
hide Configure	SRX29083879	CpG reads	Liver / SRX29083879 (CpG reads)	Schema
hide	SRX29083880	AMR	Liver / SRX29083880 (AMR)	Schema
hide Configure	SRX29083880	CpG methylation	Liver / SRX29083880 (CpG methylation)	Schema
hide	SRX29083880	PMD	Liver / SRX29083880 (PMD)	Schema
hide Configure	SRX29083880	CpG reads	Liver / SRX29083880 (CpG reads)	Schema
hide	SRX29083881	AMR	Liver / SRX29083881 (AMR)	Schema
hide Configure	SRX29083881	CpG methylation	Liver / SRX29083881 (CpG methylation)	Schema
hide	SRX29083881	PMD	Liver / SRX29083881 (PMD)	Schema
hide Configure	SRX29083881	CpG reads	Liver / SRX29083881 (CpG reads)	Schema
hide	SRX29083882	AMR	Hepa1-6 / SRX29083882 (AMR)	Schema
hide Configure	SRX29083882	CpG methylation	Hepa1-6 / SRX29083882 (CpG methylation)	Schema
hide	SRX29083882	PMD	Hepa1-6 / SRX29083882 (PMD)	Schema
hide Configure	SRX29083882	CpG reads	Hepa1-6 / SRX29083882 (CpG reads)	Schema
hide	SRX29083883	AMR	Hepa1-6 / SRX29083883 (AMR)	Schema
hide Configure	SRX29083883	CpG methylation	Hepa1-6 / SRX29083883 (CpG methylation)	Schema
hide	SRX29083883	PMD	Hepa1-6 / SRX29083883 (PMD)	Schema
hide Configure	SRX29083883	CpG reads	Hepa1-6 / SRX29083883 (CpG reads)	Schema
hide	SRX29083884	AMR	Hepa1-6 / SRX29083884 (AMR)	Schema
hide Configure	SRX29083884	CpG methylation	Hepa1-6 / SRX29083884 (CpG methylation)	Schema
hide	SRX29083884	PMD	Hepa1-6 / SRX29083884 (PMD)	Schema
hide Configure	SRX29083884	CpG reads	Hepa1-6 / SRX29083884 (CpG reads)	Schema
hide	SRX29083885	AMR	Hepa1-6 / SRX29083885 (AMR)	Schema
hide Configure	SRX29083885	CpG methylation	Hepa1-6 / SRX29083885 (CpG methylation)	Schema
hide	SRX29083885	PMD	Hepa1-6 / SRX29083885 (PMD)	Schema
hide Configure	SRX29083885	CpG reads	Hepa1-6 / SRX29083885 (CpG reads)	Schema
hide	SRX29083886	AMR	Hepa1-6 / SRX29083886 (AMR)	Schema
hide Configure	SRX29083886	CpG methylation	Hepa1-6 / SRX29083886 (CpG methylation)	Schema
hide	SRX29083886	PMD	Hepa1-6 / SRX29083886 (PMD)	Schema
hide Configure	SRX29083886	CpG reads	Hepa1-6 / SRX29083886 (CpG reads)	Schema
hide	SRX29083887	AMR	Hepa1-6 / SRX29083887 (AMR)	Schema
hide Configure	SRX29083887	CpG methylation	Hepa1-6 / SRX29083887 (CpG methylation)	Schema
hide	SRX29083887	PMD	Hepa1-6 / SRX29083887 (PMD)	Schema
hide Configure	SRX29083887	CpG reads	Hepa1-6 / SRX29083887 (CpG reads)	Schema
hide	SRX29083888	AMR	Hepa1-6 / SRX29083888 (AMR)	Schema
hide Configure	SRX29083888	CpG methylation	Hepa1-6 / SRX29083888 (CpG methylation)	Schema
hide	SRX29083888	PMD	Hepa1-6 / SRX29083888 (PMD)	Schema
hide Configure	SRX29083888	CpG reads	Hepa1-6 / SRX29083888 (CpG reads)	Schema
hide	SRX29083889	AMR	Hepa1-6 / SRX29083889 (AMR)	Schema
hide Configure	SRX29083889	CpG methylation	Hepa1-6 / SRX29083889 (CpG methylation)	Schema
hide	SRX29083889	PMD	Hepa1-6 / SRX29083889 (PMD)	Schema
hide Configure	SRX29083889	CpG reads	Hepa1-6 / SRX29083889 (CpG reads)	Schema
hide	SRX29083890	AMR	Hepa1-6 / SRX29083890 (AMR)	Schema
hide Configure	SRX29083890	CpG methylation	Hepa1-6 / SRX29083890 (CpG methylation)	Schema
hide	SRX29083890	PMD	Hepa1-6 / SRX29083890 (PMD)	Schema
hide Configure	SRX29083890	CpG reads	Hepa1-6 / SRX29083890 (CpG reads)	Schema
hide	SRX29083891	AMR	Hepa1-6 / SRX29083891 (AMR)	Schema
hide Configure	SRX29083891	CpG methylation	Hepa1-6 / SRX29083891 (CpG methylation)	Schema
hide	SRX29083891	PMD	Hepa1-6 / SRX29083891 (PMD)	Schema
hide Configure	SRX29083891	CpG reads	Hepa1-6 / SRX29083891 (CpG reads)	Schema
hide	SRX29083892	AMR	Hepa1-6 / SRX29083892 (AMR)	Schema
hide Configure	SRX29083892	CpG methylation	Hepa1-6 / SRX29083892 (CpG methylation)	Schema
hide	SRX29083892	PMD	Hepa1-6 / SRX29083892 (PMD)	Schema
hide Configure	SRX29083892	CpG reads	Hepa1-6 / SRX29083892 (CpG reads)	Schema
hide	SRX29083893	AMR	Hepa1-6 / SRX29083893 (AMR)	Schema
hide Configure	SRX29083893	CpG methylation	Hepa1-6 / SRX29083893 (CpG methylation)	Schema
hide	SRX29083893	PMD	Hepa1-6 / SRX29083893 (PMD)	Schema
hide Configure	SRX29083893	CpG reads	Hepa1-6 / SRX29083893 (CpG reads)	Schema
hide	SRX29083894	AMR	Hepa1-6 / SRX29083894 (AMR)	Schema
hide Configure	SRX29083894	CpG methylation	Hepa1-6 / SRX29083894 (CpG methylation)	Schema
hide	SRX29083894	PMD	Hepa1-6 / SRX29083894 (PMD)	Schema
hide Configure	SRX29083894	CpG reads	Hepa1-6 / SRX29083894 (CpG reads)	Schema
hide	SRX29083895	AMR	Hepa1-6 / SRX29083895 (AMR)	Schema
hide Configure	SRX29083895	CpG methylation	Hepa1-6 / SRX29083895 (CpG methylation)	Schema
hide	SRX29083895	PMD	Hepa1-6 / SRX29083895 (PMD)	Schema
hide Configure	SRX29083895	CpG reads	Hepa1-6 / SRX29083895 (CpG reads)	Schema
hide	SRX29083896	AMR	Hepa1-6 / SRX29083896 (AMR)	Schema
hide Configure	SRX29083896	CpG methylation	Hepa1-6 / SRX29083896 (CpG methylation)	Schema
hide	SRX29083896	PMD	Hepa1-6 / SRX29083896 (PMD)	Schema
hide Configure	SRX29083896	CpG reads	Hepa1-6 / SRX29083896 (CpG reads)	Schema
hide	SRX29083897	AMR	Hepa1-6 / SRX29083897 (AMR)	Schema
hide Configure	SRX29083897	CpG methylation	Hepa1-6 / SRX29083897 (CpG methylation)	Schema
hide	SRX29083897	PMD	Hepa1-6 / SRX29083897 (PMD)	Schema
hide Configure	SRX29083897	CpG reads	Hepa1-6 / SRX29083897 (CpG reads)	Schema

Study title: mRNA-Engineered CRISPR-Cas Epigenetic Editors Enable Durable and Efficient Gene Silencing in Vivo [WGBS]
SRA: SRP590495
GEO: not found
Pubmed: not found

Experiment	Label	Methylation	Coverage	HMRs	HMR size	AMRs	AMR size	PMDs	PMD size	Conversion	Details
SRX29083832	Liver	0.779	11.2	35680	1290.1	1183	994.0	1268	11854.0	0.992	title: GSM9036031 Mouse liver, Vehicle_1, Day 30, rep 1, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083833	Liver	0.781	13.0	37904	1294.4	908	922.9	3061	7200.8	0.993	title: GSM9036032 Mouse liver, Vehicle_2, Day 30, rep 2, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083834	Liver	0.784	12.1	37688	1294.7	702	934.1	1366	13248.6	0.992	title: GSM9036033 Mouse liver, Vehicle_3, Day 30, rep 3, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083835	Liver	0.771	9.6	35839	1315.3	637	931.3	1032	12846.1	0.992	title: GSM9036034 Mouse liver, Vehicle_4, Day 90, rep 1, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083836	Liver	0.772	11.2	36540	1275.1	1125	937.5	1228	12053.9	0.992	title: GSM9036035 Mouse liver, Vehicle_5, Day 90, rep 2, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083837	Liver	0.777	11.2	36157	1282.9	1010	960.1	1293	12048.2	0.992	title: GSM9036036 Mouse liver, Vehicle_6, Day 90, rep 3, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083838	Liver	0.762	9.2	31410	1376.7	805	1014.1	737	16087.6	0.992	title: GSM9036037 Mouse liver, SF01_EE_1, Day 30, rep 1, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083839	Liver	0.769	9.9	34466	1326.8	669	960.8	1083	12149.2	0.992	title: GSM9036038 Mouse liver, SF01_EE_2, Day 30, rep 2, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083840	Liver	0.765	8.9	31367	1403.0	477	968.2	1273	10805.9	0.992	title: GSM9036039 Mouse liver, SF01_EE_3, Day 30, rep 3, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083841	Liver	0.767	8.2	28367	1458.0	746	1014.4	549	19413.6	0.992	title: GSM9036040 Mouse liver, SF01_EE_4, Day 30, rep 4, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083842	Liver	0.774	9.0	29831	1386.8	959	1038.0	696	15365.4	0.992	title: GSM9036041 Mouse liver, SF01_EE_5, Day 30, rep 5, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083843	Liver	0.770	9.0	32883	1358.1	490	974.1	1144	11671.1	0.992	title: GSM9036042 Mouse liver, SF01_EE_6, Day 30, rep 6, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083844	Liver	0.770	10.1	33679	1347.3	595	950.8	1201	11896.5	0.992	title: GSM9036043 Mouse liver, SF01_EE_7, Day 90, rep 1, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083845	Liver	0.772	10.1	32460	1331.5	975	990.6	760	16862.9	0.992	title: GSM9036044 Mouse liver, SF01_EE_8, Day 90, rep 2, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083846	Liver	0.765	11.4	35281	1346.1	489	931.4	974	14050.8	0.992	title: GSM9036045 Mouse liver, SF01_EE_9, Day 90, rep 3, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083847	Liver	0.759	9.1	27505	1419.9	1359	1090.0	467	17867.5	0.991	title: GSM9036046 Mouse liver, SF01_EE_10, Day 90, rep 4, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083848	Liver	0.765	11.0	33711	1299.0	1126	962.5	974	12631.9	0.992	title: GSM9036047 Mouse liver, SF01_EE_11, Day 90, rep 5, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083849	Liver	0.778	9.9	30962	1348.0	1110	1032.9	823	14764.2	0.991	title: GSM9036048 Mouse liver, SF01_EE_12, Day 90, rep 6, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083850	Liver	0.748	14.2	37610	1182.8	2277	1007.7	1432	10918.6	0.995	title: GSM9036065 Mouse liver, Sp_EE_17, Day 120, rep 5, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083851	Liver	0.763	16.8	39780	1172.9	2330	955.1	2548	7885.0	0.995	title: GSM9036066 Mouse liver, Sp_EE_18, Day 120, rep 6, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083852	Liver	0.740	18.8	38040	1134.8	3322	1018.5	1182	11942.9	0.994	title: GSM9036067 Mouse liver, Sp_573_EE_1, Day 30, rep 1, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083853	Liver	0.763	15.9	38112	1169.1	2513	965.0	1164	12342.5	0.994	title: GSM9036068 Mouse liver, Sp_573_EE_2, Day 30, rep 2, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083854	Liver	0.764	16.6	39270	1173.9	2688	974.7	1250	12424.5	0.994	title: GSM9036069 Mouse liver, Sp_573_EE_3, Day 30, rep 3, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083855	Liver	0.775	13.8	37127	1247.5	1471	952.2	1022	13328.3	0.994	title: GSM9036070 Mouse liver, Sp_573_EE_4, Day 30, rep 4, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083856	Liver	0.766	8.7	32591	1372.9	628	957.4	1238	11423.6	0.992	title: GSM9036071 Mouse liver, Sp_573_EE_5, Day 30, rep 5, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083857	Liver	0.721	10.3	32050	1348.3	544	894.2	1049	11875.6	0.993	title: GSM9036072 Mouse liver, Sp_573_EE_6, Day 30, rep 6, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083858	Liver	0.776	12.7	35665	1267.2	1307	937.5	1005	13210.0	0.993	title: GSM9036073 Mouse liver, Sp_713_EE_1, Day 30, rep 1, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083859	Liver	0.769	11.3	35701	1271.0	868	923.1	1203	12033.3	0.994	title: GSM9036074 Mouse liver, Sp_713_EE_2, Day 30, rep 2, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083860	Liver	0.756	9.9	32945	1291.0	951	970.9	1225	11314.5	0.994	title: GSM9036075 Mouse liver, Sp_713_EE_3, Day 30, rep 3, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083861	Liver	0.782	9.7	31447	1251.9	1029	934.2	1139	14672.4	0.994	title: GSM9036076 Mouse liver, Sp_713_EE_4, Day 30, rep 4, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083862	Liver	0.764	10.1	34461	1285.4	838	960.8	1217	11748.7	0.994	title: GSM9036077 Mouse liver, Sp_713_EE_5, Day 30, rep 5, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083863	Liver	0.759	13.9	34354	1203.2	2498	1097.3	1390	10551.8	0.990	title: GSM9036078 Mouse liver, Sp_713_EE_6, Day 30, rep 6, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083864	Hepa1-6	0.743	15.4	52688	7059.0	1118	1074.3	1993	416456.0	0.992	title: GSM9036079 Mouse cell, cellMock_1, rep 1, Mus musculus, Bisulfite-Seq; {"source_name": "Hepa1-6", "cell_line": "Hepa1-6", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083865	Hepa1-6	0.748	16.1	53174	7004.3	1154	1084.2	2036	410483.9	0.992	title: GSM9036080 Mouse cell, cellMock_2, rep 2, Mus musculus, Bisulfite-Seq; {"source_name": "Hepa1-6", "cell_line": "Hepa1-6", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083866	Liver	0.783	12.2	38713	1288.9	761	939.5	1243	13123.0	0.992	title: GSM9036049 Mouse liver, Sp_EE_1, Day 30, rep 1, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083867	Liver	0.787	11.5	39367	1300.7	637	939.8	1305	13369.8	0.992	title: GSM9036050 Mouse liver, Sp_EE_2, Day 30, rep 2, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083868	Liver	0.783	8.5	30090	1445.7	850	1076.1	702	14858.3	0.991	title: GSM9036051 Mouse liver, Sp_EE_3, Day 30, rep 3, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083869	Liver	0.785	11.0	36318	1332.4	755	975.2	1164	12242.9	0.992	title: GSM9036052 Mouse liver, Sp_EE_4, Day 30, rep 4, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083870	Liver	0.785	10.5	35189	1347.5	809	970.0	1204	11927.5	0.992	title: GSM9036053 Mouse liver, Sp_EE_5, Day 30, rep 5, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083871	Liver	0.774	11.8	38362	1256.3	1158	985.6	1289	11756.9	0.994	title: GSM9036054 Mouse liver, Sp_EE_6, Day 30, rep 6, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083872	Liver	0.784	8.5	33378	1403.2	613	988.3	811	17333.6	0.992	title: GSM9036055 Mouse liver, Sp_EE_7, Day 90, rep 1, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083873	Liver	0.789	8.3	31164	1437.1	634	985.7	750	17596.2	0.990	title: GSM9036056 Mouse liver, Sp_EE_8, Day 90, rep 2, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083874	Liver	0.783	9.0	32662	1382.3	865	1019.8	972	15830.0	0.992	title: GSM9036057 Mouse liver, Sp_EE_9, Day 90, rep 3, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083875	Liver	0.784	8.0	30704	1441.0	739	1631.8	487	21865.6	0.991	title: GSM9036058 Mouse liver, Sp_EE_10, Day 90, rep 4, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083876	Liver	0.787	10.7	36255	1338.7	713	973.1	1233	12262.6	0.992	title: GSM9036059 Mouse liver, Sp_EE_11, Day 90, rep 5, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083877	Liver	0.767	8.7	33489	1392.1	492	996.7	1325	11085.4	0.992	title: GSM9036060 Mouse liver, Sp_EE_12, Day 90, rep 6, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083878	Liver	0.773	9.0	31720	1403.0	734	978.4	623	17371.1	0.992	title: GSM9036061 Mouse liver, Sp_EE_13, Day 120, rep 1, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083879	Liver	0.774	6.1	26162	1549.4	622	1065.3	373	24081.2	0.991	title: GSM9036062 Mouse liver, Sp_EE_14, Day 120, rep 2, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083880	Liver	0.784	12.1	33419	1284.2	1589	1190.2	1458	10586.9	0.994	title: GSM9036063 Mouse liver, Sp_EE_15, Day 120, rep 3, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083881	Liver	0.773	8.6	29111	1437.4	798	1025.2	754	14006.1	0.994	title: GSM9036064 Mouse liver, Sp_EE_16, Day 120, rep 4, Mus musculus, Bisulfite-Seq; {"source_name": "liver", "tissue": "liver", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083882	Hepa1-6	0.748	14.6	51241	6974.7	1106	1127.4	2047	404801.7	0.992	title: GSM9036081 Mouse cell, cellMock_3, rep 3, Mus musculus, Bisulfite-Seq; {"source_name": "Hepa1-6", "cell_line": "Hepa1-6", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083883	Hepa1-6	0.748	16.3	49065	7677.9	1020	1104.8	1978	418696.4	0.994	title: GSM9036082 Mouse cell, cellSF01_EE_1, rep 1, Mus musculus, Bisulfite-Seq; {"source_name": "Hepa1-6", "cell_line": "Hepa1-6", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083884	Hepa1-6	0.748	16.8	51115	7723.0	891	1069.6	1953	428066.7	0.995	title: GSM9036083 Mouse cell, cellSF01_EE_2, rep 2, Mus musculus, Bisulfite-Seq; {"source_name": "Hepa1-6", "cell_line": "Hepa1-6", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083885	Hepa1-6	0.737	10.3	45980	7959.8	362	1027.9	1812	461076.4	0.993	title: GSM9036084 Mouse cell, cellSF01_EE_3, rep 3, Mus musculus, Bisulfite-Seq; {"source_name": "Hepa1-6", "cell_line": "Hepa1-6", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083886	Hepa1-6	0.748	10.3	45417	7891.5	458	1046.2	1580	536400.6	0.993	title: GSM9036085 Mouse cell, cellSF01_EE_4, rep 4, Mus musculus, Bisulfite-Seq; {"source_name": "Hepa1-6", "cell_line": "Hepa1-6", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083887	Hepa1-6	0.741	11.1	47362	7976.6	482	1007.6	1876	447850.0	0.993	title: GSM9036086 Mouse cell, cellSF01_EE_5, rep 5, Mus musculus, Bisulfite-Seq; {"source_name": "Hepa1-6", "cell_line": "Hepa1-6", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083888	Hepa1-6	0.719	11.5	47515	8287.6	369	962.4	1858	451312.8	0.994	title: GSM9036087 Mouse cell, cellSF01_EE_6, rep 6, Mus musculus, Bisulfite-Seq; {"source_name": "Hepa1-6", "cell_line": "Hepa1-6", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083889	Hepa1-6	0.762	17.3	48076	8453.3	865	1066.8	1899	450536.2	0.992	title: GSM9036088 Mouse cell, cellSp_EE_1, rep 1, Mus musculus, Bisulfite-Seq; {"source_name": "Hepa1-6", "cell_line": "Hepa1-6", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083890	Hepa1-6	0.769	13.8	45423	8016.1	787	1101.6	1531	554161.5	0.992	title: GSM9036089 Mouse cell, cellSp_EE_2, rep 2, Mus musculus, Bisulfite-Seq; {"source_name": "Hepa1-6", "cell_line": "Hepa1-6", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083891	Hepa1-6	0.736	12.8	47240	8881.0	414	986.3	1848	475461.9	0.992	title: GSM9036090 Mouse cell, cellSp_EE_3, rep 3, Mus musculus, Bisulfite-Seq; {"source_name": "Hepa1-6", "cell_line": "Hepa1-6", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083892	Hepa1-6	0.755	16.6	48372	8406.0	850	1055.1	1901	451549.8	0.994	title: GSM9036091 Mouse cell, cellSp_573_EE_1, rep 1, Mus musculus, Bisulfite-Seq; {"source_name": "Hepa1-6", "cell_line": "Hepa1-6", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083893	Hepa1-6	0.748	14.8	48200	8556.0	699	1014.0	1919	452165.2	0.994	title: GSM9036092 Mouse cell, cellSp_573_EE_2, rep 2, Mus musculus, Bisulfite-Seq; {"source_name": "Hepa1-6", "cell_line": "Hepa1-6", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083894	Hepa1-6	0.763	12.4	45454	8136.1	665	1099.8	1537	560482.1	0.993	title: GSM9036093 Mouse cell, cellSp_573_EE_3, rep 3, Mus musculus, Bisulfite-Seq; {"source_name": "Hepa1-6", "cell_line": "Hepa1-6", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083895	Hepa1-6	0.752	14.8	47341	8830.7	626	1050.4	1927	456511.0	0.992	title: GSM9036094 Mouse cell, cellSp_713_EE_1, rep 1, Mus musculus, Bisulfite-Seq; {"source_name": "Hepa1-6", "cell_line": "Hepa1-6", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083896	Hepa1-6	0.764	18.2	46587	8749.0	865	1095.4	1905	452775.0	0.992	title: GSM9036095 Mouse cell, cellSp_713_EE_2, rep 2, Mus musculus, Bisulfite-Seq; {"source_name": "Hepa1-6", "cell_line": "Hepa1-6", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29083897	Hepa1-6	0.746	20.5	47309	8500.7	1135	1127.4	1947	438495.4	0.994	title: GSM9036096 Mouse cell, cellSp_713_EE_3, rep 3, Mus musculus, Bisulfite-Seq; {"source_name": "Hepa1-6", "cell_line": "Hepa1-6", "geo_loc_name": "missing", "collection_date": "missing"}

Methods

All analysis was done using a bisulfite sequnecing data analysis pipeline DNMTools developed in the Smith lab at USC.

Mapping reads from bisulfite sequencing: Bisulfite treated reads are mapped to the genomes with the abismal program. Input reads are filtered by their quality, and adapter sequences in the 3' end of reads are trimmed. This is done with cutadapt. Uniquely mapped reads with mismatches/indels below given threshold are retained. For pair-end reads, if the two mates overlap, the overlapping part of the mate with lower quality is discarded. After mapping, we use the format command in dnmtools to merge mates for paired-end reads. We use the dnmtools uniq command to randomly select one from multiple reads mapped exactly to the same location. Without random oligos as UMIs, this is our best indication of PCR duplicates.

Estimating methylation levels: After reads are mapped and filtered, the dnmtools counts command is used to obtain read coverage and estimate methylation levels at individual cytosine sites. We count the number of methylated reads (those containing a C) and the number of unmethylated reads (those containing a T) at each nucleotide in a mapped read that corresponds to a cytosine in the reference genome. The methylation level of that cytosine is estimated as the ratio of methylated to total reads covering that cytosine. For cytosines in the symmetric CpG sequence context, reads from the both strands are collapsed to give a single estimate. Very rarely do the levels differ between strands (typically only if there has been a substitution, as in a somatic mutation), and this approach gives a better estimate.

Bisulfite conversion rate: The bisulfite conversion rate for an experiment is estimated with the dnmtools bsrate command, which computes the fraction of successfully converted nucleotides in reads (those read out as Ts) among all nucleotides in the reads mapped that map over cytosines in the reference genome. This is done either using a spike-in (e.g., lambda), the mitochondrial DNA, or the nuclear genome. In the latter case, only non-CpG sites are used. While this latter approach can be impacted by non-CpG cytosine methylation, in practice it never amounts to much.

Identifying hypomethylated regions (HMRs): In most mammalian cells, the majority of the genome has high methylation, and regions of low methylation are typically the interesting features. (This seems to be true for essentially all healthy differentiated cell types, but not cells of very early embryogenesis, various germ cells and precursors, and placental lineage cells.) These are valleys of low methylation are called hypomethylated regions (HMR) for historical reasons. To identify the HMRs, we use the dnmtools hmr command, which uses a statistical model that accounts for both the methylation level fluctations and the varying amounts of data available at each CpG site.

Partially methylated domains: Partially methylated domains are large genomic regions showing partial methylation observed in immortalized cell lines and cancerous cells. The pmd program is used to identify PMDs.

Allele-specific methylation: Allele-Specific methylated regions refers to regions where the parental allele is differentially methylated compared to the maternal allele. The program allelic is used to compute allele-specific methylation score can be computed for each CpG site by testing the linkage between methylation status of adjacent reads, and the program amrfinder is used to identify regions with allele-specific methylation.

For more detailed description of the methods of each step, please refer to the DNMTools documentation.