Control track and group visibility more selectively below.
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| Cow methylome studies |
| Cow methylome studies |
| SRP289575 |
| Dynamic regulation of regulatory elements in rumen development [Rumen] |
| SRP254023 |
| Analyses of methylomes of multiple tissues in cattle [Adipose, Blood, Heart, Ileum, Kidney, Ldorsi, Liver, Lung, Ovary, Placenta, Rumen, Spleen, Uterus] |
| SRP253271 |
| Analyses of methylomes of Bones in cattle [Bone] |
| SRP049936 |
| DNA methylation in mammalian placentas [Cerebrum, Cord Blood, Extraembryonic Membrane, Placenta, Trophoblasts] |
| SRP242537 |
| DNA methylation changes during preimplantation development reveal inter species-differences and reprogramming events at imprinted genes [BS-Seq] [2-4 cell embryo, 8-16 cell embryo, Blastocyst, Morula, Oocyte, Sperm] |
| SRP238442 |
| Integration of whole-genome DNA methylation data with RNA sequencing data to identify markers for bull fertility [Sperm] |
| SRP237841 |
| scWGBS fresh bovine GV oocyte sample 2 [GV oocyte] |
| SRP236906 |
| scWGBS vitrified bovine GV oocyte sample 3 [GV oocyte] |
| SRP236062 |
| scWGBS bovine MII oocyte derived from vitrified GV oocyte sample 2 [MII oocyte] |
| SRP235962 |
| scWGBS vitrified bovine GV oocyte sample 2 [GV oocyte] |
| SRP235169 |
| scWGBS vitrified bovine GV oocyte sample 1 [GV oocyte] |
| SRP235167 |
| scWGBS fresh bovine GV oocyte sample 3 [GV oocyte] |
| SRP234847 |
| scWGBS fresh bovine GV oocyte sample 1 [GV oocyte] |
| SRP200197 |
| Investigation of genomic imprinting in cattle [Blood, Oocytes, Sperm] |
| SRP199656 |
| Divergences of sperm DNA methylomes between monozygotic twin seed bulls reveal fertility-related genes (WGBS) [Sperm] |
| SRP197316 |
| Raw sequence reads of whole genome DNA methylation sequencing of bovine blastocyst derived from in vivo, fresh and vitrified oocytes after IVF [IVF blastocyst 1, IVF blastocyst 2, IVF blastocyst 3, V-IVF blastocyst 1, V-IVF blastocyst 2, V-IVF blastocyst 3, in vivo blastocyst 1, in vivo blastocyst 2, in vivo blastocyst 3] |
| SRP192453 |
| Establishment of bovine expanded potential stem cells [Embryonic Stem, Induced Pluripotent Stem, Somatic] |
| SRP190079 |
| Whole Genome Bisulfite Sequecing of Yaks, Tibetan cattles, Sanjiang cattles and Holstein cows. [Breast, Lung, Muscle] |
| SRP179788 |
| Bos taurus breed:Holstein Epigenomics [Blood] |
| SRP166801 |
| Methylome Dynamics of Bovine Gametes and In Vivo Early Embryos [Sperm] |
| SRP162610 |
| DNA methylation of cattle sperms under hot and cool environments [Sperm] |
| SRP159181 |
| Comparative sperm methylome analysis provide insights into complex phenotypes and epigenome evolution [Sperm] |
| SRP154033 |
| Maternal methionine supplementation alters the epigenome of the offspring [Bisulfite-Seq] [Longissimus Dorsi] |
| SRP132590 |
| The bovine alveolar macrophage (bAM) DNA methylome is resilient to infection with Mycobacterium bovis [Alveolar Macrophages] |
| SRP124288 |
| Genome-wide sequencing and comparative profiling of cattle sperm DNA methylome [Blood, Brain, Mammary Gland, Sperm] |
| SRP588790 |
| Tributyltin chloride alters the structural, genomic, and epigenomic integrity of postejaculatory mammalian sperm [Sperm] |
| SRP572682 |
| Mycoplasma bovis nucleomodulin MbovP202 modulates DNA methylation in BoMac cells [Bovine Peritoneal Macrophages] |
| SRP106881 |
| Whole Genome Bisulfite Sequencing of Longissimus Dorsi Muscles between Japanese Black (Wagyu) and Chinese Red Steppes Cattle [Muscle] |
| SRP564298 |
| Bos taurus Epigenomics [Blood] |
| SRP524654 |
| daily liver and mammary WGBS RNA-SEQ and atac-seq dataset [Liver, Mammary] |
| SRP502696 |
| Epigenetic Basis for the Establishment of Ruminal Tissue-Specific Functions (BS-seq) [Bovine Expanded Pluripotent Stem Cell, Bovine Induced Pluripotent Stem Cell, Forebrain, Heart, Hindbrain, Kidney, Liver, Lung, Rumen, Skeletal Muscle, Testis] |
| SRP486291 |
| The multiomics data on gametes and early embryos in bovine and porcine [Oocyte] |
| SRP472636 |
| Mixed-Lineage Leukemia 1 Inhibition Enhances the Differentiation Potential of Bovine Embryonic Stem Cells by Increasing H3K4 Mono-Methylation at Active Promoters. (BS-seq) [Bovine Fetal Fibroblasts, ESC] |
| SRP257404 |
| Transcriptome profiling of two purebred cattle and their crossbreds [Liver] |
| SRP435692 |
| Whole genome DNA methylation sequencing in relation to Staphylococcus chromogenes subclinical mastitis [Milk Somatic] |
| SRP417956 |
| Epigenomics of metabolic organs from in vitro or in vivo-produced dairy male calves [Adrenal, Hypothalamus, Liver, Muscle, Pituitary, Testicle] |
| SRP417391 |
| Cold exposure impacts DNA methylation patterns in cattle sperm [Sperm] |
| SRP412967 |
| Establishment of bovine trophoblast stem cells [WGBS] [trophectoderm (TE), trophoblast stem cells (TSCs)] |
| SRP408130 |
| Maternal diet induces persistent DNA methylation changes in the muscle of beef calves [Loin Muscle] |
| SRP394828 |
| CpG methylation of epididymal caput, corpus, cauda isolate bull sperm [Sperm] |
| SRP392500 |
| Comparative epigenomic analyses of DNA methylomes and gene expression during ruminant evolution [Brain, Muscle, Sperm] |
| SRP387792 |
| bovine methylation sequencing [Blood] |
| SRP382771 |
| Comparative analyses of DNA methylomes in the liver among three ruminants [Liver] |
| SRP365107 |
| Spontaneous and ART-induced large offspring syndrome: similarities and differences in DNA methylome [Blood, Ear, Muscle, Tongue] |
| SRP355367 |
| Whole genome bisulfite sequencing of X sperm and Y sperm for Holstein bulls [Sperm] |
| SRP349441 |
| Genome-wide DNA-methylation analysis of fat-1 transgenic bovine fetal fibroblasts and wild-type [Fibroblast] |
| SRP329323 |
| Whole genome bisulfite sequencing of muscle, liver, brain tissues in cattle [Cerebral Cortex, Liver, Longissimus Dorsi Muscle] |
| SRP329307 |
| Whole genome bisulfite sequencing of rumen, muscle, placenta, sperm tissues in cattle [Placenta, Rumen, Skeletal Muscle, Sperm] |
| SRP327608 |
| WGBS for holstein jejunum associated with paratuberculosis [Jejunum] |
| SRP322041 |
| Comparing the whole genome methylation landscape of dairy calf blood cells revealed potential intergenerational inheritance of the maternal metabolic status [Blood] |
| SRP321573 |
| Conservation and divergence of DNA methylation patterns and functions in vertebrates [Primary Dermal Fibroblasts, Psoas Muscle] |
| ERP116794 |
| Whole genome bisulfite sequencing of bovine morula derived from metabolically divergent dairy cows [Morula] |
| ERP116535 |
| Whole genome bisulfite sequencing of bovine oocytes from metabolically divergent lactating cows and nulliparous heifers [Oocytes] |
| ERP152810 |
| Mining the Methylome for New Insights into Bovine Tuberculosis. [Blood] |
| Common |
| Common methbase tracks for the bosTau9 assembly |
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| Base Position |
| Chromosome position in bases. (Clicks here zoom in 3x) |
| Assembly |
| Assembly from Fragments |
| Gap |
| Gap Locations |
| GC Percent |
| GC Percent in 5-Base Windows |
| INSDC |
| Accession at INSDC - International Nucleotide Sequence Database Collaboration |
| RefSeq Acc |
| RefSeq Accession |
| Restr Enzymes |
| Restriction Enzymes from REBASE |
| Short Match |
| Perfect Matches to Short Sequence () |
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| NCBI RefSeq |
| RefSeq genes from NCBI |
| AUGUSTUS |
| AUGUSTUS ab initio gene predictions v3.1 |
| CRISPR Targets |
| CRISPR/Cas9 -NGG Targets, whole genome |
| Ensembl Genes |
| Ensembl Genes |
| Genscan Genes |
| Genscan Gene Predictions |
| Other RefSeq |
| Non-Cow RefSeq Genes |
| TOGA vs. hg38 |
| TOGA annotations using human/hg38 as reference |
| TransMap V5 |
| TransMap Alignments Version 5 |
| TransMap Ensembl |
| TransMap Ensembl and GENCODE Mappings Version 5 |
| TransMap RefGene |
| TransMap RefSeq Gene Mappings Version 5 |
| TransMap RNA |
| TransMap GenBank RNA Mappings Version 5 |
| TransMap ESTs |
| TransMap EST Mappings Version 5 |
| UniProt |
| UniProt SwissProt/TrEMBL Protein Annotations |
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| Cow ESTs |
| Cow ESTs Including Unspliced |
| Cow mRNAs |
| Cow mRNAs from GenBank |
| Spliced ESTs |
| Cow ESTs That Have Been Spliced |
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| CpG Islands |
| CpG Islands (Islands < 300 Bases are Light Green) |
| CpG Islands |
| CpG Islands (Islands < 300 Bases are Light Green) |
| Unmasked CpG |
| CpG Islands on All Sequence (Islands < 300 Bases are Light Green) |
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| ClinVar Lift |
| Human ClinVar variants lifted to Cow |
| mm10 ChainNet |
| Mouse (Dec. 2011 (GRCm38/mm10)), Chain and Net Alignments |
| Mouse Chain/Net |
| Mouse (Jun. 2020 (GRCm39/mm39)), Chain and Net Alignments |
| Human Chain/Net |
| Human (Dec. 2013 (GRCh38/hg38)), Chain and Net Alignments |
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| RepeatMasker |
| Repeating Elements by RepeatMasker |
| updated
EVA SNP |
| Short Genetic Variants from European Variant Archive |
| Interrupted Rpts |
| Fragments of Interrupted Repeats Joined by RepeatMasker ID |
| Microsatellite |
| Microsatellites - Di-nucleotide and Tri-nucleotide Repeats |
| Simple Repeats |
| Simple Tandem Repeats by TRF |
| WM + SDust |
| Genomic Intervals Masked by WindowMasker + SDust |
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