Human methylome studies SRP000941 Track Settings
Study title: UCSD Human Reference Epigenome Mapping ProjectSRA: SRP000941 GEO: GSE16256 Pubmed: 19829295
Experiment
Label
Methylation
Coverage
HMRs
HMR size
AMRs
AMR size
PMDs
PMD size
Conversion
Details
SRX006239 ESC
0.818
8.6
29924
1374.4
1409
22275.4
1791
12530.1
0.980
title: Whole genome shotgun bisulfite sequencing of the H1 cell line; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Thomson Laboratory", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "H1", "LINEAGE": "NA", "BATCH": "#2", "DIFFERENTIATION_STAGE": "embryonic stem cell", "DIFFERENTIATION_METHOD": "NA", "PASSAGE": "27", "MEDIUM": "TeSR", "sex": "male", "sample_term_id": "EFO_0003042"}
SRX006240 ESC
0.827
7.3
29670
1395.0
1083
28037.2
1805
12034.3
0.980
title: Whole genome shotgun bisulfite sequencing of the H1 cell line; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Thomson Laboratory", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "H1", "LINEAGE": "NA", "BATCH": "#2", "DIFFERENTIATION_STAGE": "embryonic stem cell", "DIFFERENTIATION_METHOD": "NA", "PASSAGE": "27", "MEDIUM": "TeSR", "sex": "male", "sample_term_id": "EFO_0003042"}
SRX006782 ESC
0.843
6.3
24528
1461.5
529
53377.7
1510
19542.4
0.980
title: Whole genome shotgun bisulfite sequencing of the H1 cell line; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Thomson Laboratory", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "H1", "LINEAGE": "NA", "BATCH": "#1", "DIFFERENTIATION_STAGE": "embryonic stem cell", "DIFFERENTIATION_METHOD": "NA", "PASSAGE": "25", "MEDIUM": "TeSR", "sex": "male", "sample_term_id": "EFO_0003042"}
SRX006783 IMR90
0.672
6.9
57627
10359.5
855
35438.8
1936
621376.5
0.996
title: Whole genome shotgun bisulfite sequencing of the IMR90 cell line; {"sex": "female", "biomaterial_provider": "ATCC", "DIFFERENTIATION_METHOD": "NA", "MOLECULE": "genomic DNA", "sample_term_id": "EFO_0001196", "PASSAGE": "4", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "IMR90", "DIFFERENTIATION_STAGE": "Fetal lung fibroblast", "MEDIUM": "Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)", "disease": "None", "BATCH": "#1", "cell_type": "IMR90 cells", "LINEAGE": "NA"}
SRX006784 IMR90
0.675
6.6
57157
10432.1
723
41532.7
1937
620468.5
0.996
title: Whole genome shotgun bisulfite sequencing of the IMR90 cell line; {"sex": "female", "biomaterial_provider": "ATCC", "DIFFERENTIATION_METHOD": "NA", "MOLECULE": "genomic DNA", "sample_term_id": "EFO_0001196", "PASSAGE": "4", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "IMR90", "DIFFERENTIATION_STAGE": "Fetal lung fibroblast", "MEDIUM": "Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)", "disease": "None", "BATCH": "#1", "cell_type": "IMR90 cells", "LINEAGE": "NA"}
SRX006785 IMR90
0.684
2.1
44821
10221.1
178
155724.0
1276
891963.3
0.996
title: Whole genome shotgun bisulfite sequencing of the IMR90 cell line; {"sex": "female", "biomaterial_provider": "ATCC", "DIFFERENTIATION_METHOD": "NA", "MOLECULE": "genomic DNA", "sample_term_id": "EFO_0001196", "PASSAGE": "4", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "IMR90", "DIFFERENTIATION_STAGE": "Fetal lung fibroblast", "MEDIUM": "Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)", "disease": "None", "BATCH": "#1", "cell_type": "IMR90 cells", "LINEAGE": "NA"}
SRX006786 IMR90
0.675
7.1
57550
10640.8
1084
28524.6
1950
623323.8
0.995
title: Whole genome shotgun bisulfite sequencing of the IMR90 cell line; {"sex": "female", "biomaterial_provider": "ATCC", "DIFFERENTIATION_METHOD": "NA", "MOLECULE": "genomic DNA", "sample_term_id": "EFO_0001196", "PASSAGE": "5", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "IMR90", "DIFFERENTIATION_STAGE": "Fetal lung fibroblast", "MEDIUM": "Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)", "disease": "None", "BATCH": "#2", "cell_type": "IMR90 cells", "LINEAGE": "NA"}
SRX006787 IMR90
0.676
8.3
60160
10184.6
1690
19067.7
1995
612219.1
0.995
title: Whole genome shotgun bisulfite sequencing of the IMR90 cell line; {"sex": "female", "biomaterial_provider": "ATCC", "DIFFERENTIATION_METHOD": "NA", "MOLECULE": "genomic DNA", "sample_term_id": "EFO_0001196", "PASSAGE": "5", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "IMR90", "DIFFERENTIATION_STAGE": "Fetal lung fibroblast", "MEDIUM": "Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)", "disease": "None", "BATCH": "#2", "cell_type": "IMR90 cells", "LINEAGE": "NA"}
SRX006788 IMR90
0.682
2.8
48567
10828.7
239
117258.1
1439
814241.5
0.996
title: Whole genome shotgun bisulfite sequencing of the IMR90 cell line; {"sex": "female", "biomaterial_provider": "ATCC", "DIFFERENTIATION_METHOD": "NA", "MOLECULE": "genomic DNA", "sample_term_id": "EFO_0001196", "PASSAGE": "5", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "IMR90", "DIFFERENTIATION_STAGE": "Fetal lung fibroblast", "MEDIUM": "Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)", "disease": "None", "BATCH": "#2", "cell_type": "IMR90 cells", "LINEAGE": "NA"}
SRX006789 ESC
0.832
6.1
23312
1510.7
469
61704.8
1466
15963.1
0.972
title: Whole genome shotgun bisulfite sequencing of the H1 cell line; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Thomson Laboratory", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "H1", "LINEAGE": "NA", "BATCH": "#1", "DIFFERENTIATION_STAGE": "embryonic stem cell", "DIFFERENTIATION_METHOD": "NA", "PASSAGE": "25", "MEDIUM": "TeSR", "sex": "male", "sample_term_id": "EFO_0003042"}
SRX027685 ESC
0.821
14.8
40630
1024.5
7448
5161.4
2123
13647.9
0.988
title: Whole genome shotgun bisulfite sequencing of the H1 cell line treated with BMP4 for 5 days; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Thomson Laboratory", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "H1", "LINEAGE": "NA", "DIFFERENTIATION_STAGE": "embryonic stem cell differentiated by treatment with BMP4", "DIFFERENTIATION_METHOD": "H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days", "PASSAGE": "27, including 16 passages in TeSR", "MEDIUM": "TeSR", "sex": "male", "BATCH": "Replicate 1", "sample_term_id": "UBERON_0000088"}
SRX027686 ESC
0.825
6.2
33031
1214.2
1179
24757.3
1136
17212.7
0.989
title: Whole genome shotgun bisulfite sequencing of the H1 cell line treated with BMP4 for 5 days; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Thomson Laboratory", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "H1", "LINEAGE": "NA", "DIFFERENTIATION_STAGE": "embryonic stem cell differentiated by treatment with BMP4", "DIFFERENTIATION_METHOD": "H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days", "PASSAGE": "27, including 16 passages in TeSR", "MEDIUM": "TeSR", "sex": "male", "BATCH": "Replicate 1", "sample_term_id": "UBERON_0000088"}
SRX027687 ESC
0.808
5.6
31372
1268.0
1057
27141.5
954
22173.1
0.985
title: Whole genome shotgun bisulfite sequencing of the H1 cell line treated with BMP4 for 5 days; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Thomson Laboratory", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "H1", "LINEAGE": "NA", "DIFFERENTIATION_STAGE": "embryonic stem cell differentiated by treatment with BMP4", "DIFFERENTIATION_METHOD": "H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days", "PASSAGE": "27, including 16 passages in TeSR", "MEDIUM": "TeSR", "sex": "male", "BATCH": "Replicate 1", "sample_term_id": "UBERON_0000088"}
SRX027688 ESC
0.813
6.8
33523
1199.3
1629
1821.6
963
16372.5
0.990
title: Whole genome shotgun bisulfite sequencing of the H1 cell line treated with BMP4 for 5 days; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Thomson Laboratory", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "H1", "LINEAGE": "NA", "DIFFERENTIATION_STAGE": "embryonic stem cell differentiated by treatment with BMP4", "DIFFERENTIATION_METHOD": "H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days", "PASSAGE": "25, including 10 passages in TeSR", "MEDIUM": "TeSR", "sex": "male", "BATCH": "Replicate 2", "sample_term_id": "UBERON_0000088"}
SRX027689 ESC
0.810
6.9
33379
1202.5
1734
1907.0
1006
15839.1
0.990
title: Whole genome shotgun bisulfite sequencing of the H1 cell line treated with BMP4 for 5 days; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Thomson Laboratory", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "H1", "LINEAGE": "NA", "DIFFERENTIATION_STAGE": "embryonic stem cell differentiated by treatment with BMP4", "DIFFERENTIATION_METHOD": "H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days", "PASSAGE": "25, including 10 passages in TeSR", "MEDIUM": "TeSR", "sex": "male", "BATCH": "Replicate 2", "sample_term_id": "UBERON_0000088"}
SRX027690 ESC
0.810
7.4
34451
1175.3
1910
11195.0
1042
15815.7
0.990
title: Whole genome shotgun bisulfite sequencing of the H1 cell line treated with BMP4 for 5 days; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Thomson Laboratory", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "H1", "LINEAGE": "NA", "DIFFERENTIATION_STAGE": "embryonic stem cell differentiated by treatment with BMP4", "DIFFERENTIATION_METHOD": "H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days", "PASSAGE": "25, including 10 passages in TeSR", "MEDIUM": "TeSR", "sex": "male", "BATCH": "Replicate 2", "sample_term_id": "UBERON_0000088"}
SRX043404 ESC
0.843
6.5
36123
1125.3
836
23799.5
1534
37623.6
0.994
title: Whole genome shotgun bisulfite sequencing of the H1 cell line differentiated into neural progenitor cells; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Thomson Laboratory", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "H1", "LINEAGE": "NA", "DIFFERENTIATION_STAGE": "embryonic stem cell differentiated into neural progenitor cells", "DIFFERENTIATION_METHOD": "H1 cells were differentiated by culturing in insulin, SB, Noggin", "PASSAGE": "25", "MEDIUM": "TeSR", "sex": "male", "BATCH": "Replicate 1", "sample_term_id": "CL_0000047"}
SRX043405 ESC
0.846
6.7
36683
1113.2
884
22944.5
1466
39521.1
0.994
title: Whole genome shotgun bisulfite sequencing of the H1 cell line differentiated into neural progenitor cells; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Thomson Laboratory", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "H1", "LINEAGE": "NA", "DIFFERENTIATION_STAGE": "embryonic stem cell differentiated into neural progenitor cells", "DIFFERENTIATION_METHOD": "H1 cells were differentiated by culturing in insulin, SB, Noggin", "PASSAGE": "25", "MEDIUM": "TeSR", "sex": "male", "BATCH": "Replicate 1", "sample_term_id": "CL_0000047"}
SRX043406 ESC
0.841
6.8
36933
1103.6
993
29544.2
1389
40023.8
0.994
title: Whole genome shotgun bisulfite sequencing of the H1 cell line differentiated into neural progenitor cells; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Thomson Laboratory", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "H1", "LINEAGE": "NA", "DIFFERENTIATION_STAGE": "embryonic stem cell differentiated into neural progenitor cells", "DIFFERENTIATION_METHOD": "H1 cells were differentiated by culturing in insulin, SB, Noggin", "PASSAGE": "25", "MEDIUM": "TeSR", "sex": "male", "BATCH": "Replicate 1", "sample_term_id": "CL_0000047"}
SRX043407 ESC
0.855
10.6
40586
1039.5
1791
17998.5
2217
36784.7
0.994
title: Whole genome shotgun bisulfite sequencing of the H1 cell line differentiated into neural progenitor cells; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Thomson Laboratory", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "H1", "LINEAGE": "NA", "DIFFERENTIATION_STAGE": "embryonic stem cell differentiated into neural progenitor cells", "DIFFERENTIATION_METHOD": "H1 cells were differentiated by culturing in insulin, SB, Noggin", "PASSAGE": "27", "MEDIUM": "TeSR", "sex": "male", "BATCH": "Replicate 2", "sample_term_id": "CL_0000047"}
SRX043408 ESC
0.852
8.6
37974
1085.2
1271
24438.0
2093
35347.3
0.994
title: Whole genome shotgun bisulfite sequencing of the H1 cell line differentiated into neural progenitor cells; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Thomson Laboratory", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "H1", "LINEAGE": "NA", "DIFFERENTIATION_STAGE": "embryonic stem cell differentiated into neural progenitor cells", "DIFFERENTIATION_METHOD": "H1 cells were differentiated by culturing in insulin, SB, Noggin", "PASSAGE": "27", "MEDIUM": "TeSR", "sex": "male", "BATCH": "Replicate 2", "sample_term_id": "CL_0000047"}
SRX056687 Cell Line
0.827
22.5
40442
1078.9
15850
3399.6
4000
7598.0
0.984
title: Whole genome shotgun bisulfite sequencing of the iPS cell line clone 19.11 derived from reprogramming of foreskin fibroblasts; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Thomson Laboratory", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "iPS DF 19.11", "LINEAGE": "NA", "DIFFERENTIATION_STAGE": "induced pluripotent stem cell", "DIFFERENTIATION_METHOD": "NA", "PASSAGE": "32", "MEDIUM": "TeSR", "sex": "male", "BATCH": "Replicate 1", "sample_term_id": "NTR_0001173"}
SRX056688 Cell Line
0.822
17.2
38591
1095.1
9293
4612.7
3752
7318.7
0.983
title: Whole genome shotgun bisulfite sequencing of the iPS cell line clone 19.11 derived from reprogramming of foreskin fibroblasts; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Thomson Laboratory", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "iPS DF 19.11", "LINEAGE": "NA", "DIFFERENTIATION_STAGE": "induced pluripotent stem cell", "DIFFERENTIATION_METHOD": "NA", "PASSAGE": "32", "MEDIUM": "TeSR", "sex": "male", "BATCH": "Replicate 1", "sample_term_id": "NTR_0001173"}
SRX056691 Cell Line
0.836
17.7
38554
1114.4
6622
5953.0
4266
7294.1
0.983
title: Whole genome shotgun bisulfite sequencing of the iPS cell line clone 6.9 derived from reprogramming of foreskin fibroblasts; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Thomson Laboratory", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "iPS DF 6.9", "LINEAGE": "NA", "DIFFERENTIATION_STAGE": "induced pluripotent stem cell", "DIFFERENTIATION_METHOD": "NA", "PASSAGE": "33", "MEDIUM": "TeSR", "sex": "male", "BATCH": "Replicate 1", "sample_term_id": "NTR_0001172"}
SRX056692 Cell Line
0.835
13.5
36538
1148.2
3585
9609.5
4199
7067.0
0.983
title: Whole genome shotgun bisulfite sequencing of the iPS cell line clone 6.9 derived from reprogramming of foreskin fibroblasts; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Thomson Laboratory", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "iPS DF 6.9", "LINEAGE": "NA", "DIFFERENTIATION_STAGE": "induced pluripotent stem cell", "DIFFERENTIATION_METHOD": "NA", "PASSAGE": "33", "MEDIUM": "TeSR", "sex": "male", "BATCH": "Replicate 1", "sample_term_id": "NTR_0001172"}
SRX056693 ESC
0.842
5.3
31529
1266.5
754
2156.9
1691
36467.5
0.989
title: Whole genome shotgun bisulfite sequencing of the H9 cell line; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Thomson Laboratory", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "H9", "LINEAGE": "NA", "DIFFERENTIATION_STAGE": "embryonic stem cell", "DIFFERENTIATION_METHOD": "NA", "PASSAGE": "42", "MEDIUM": "TeSR", "sex": "female", "BATCH": "Replicate 1", "sample_term_id": "NTR_0000838"}
SRX056694 ESC
0.844
12.9
38972
1079.3
3622
9244.5
4552
15215.3
0.989
title: Whole genome shotgun bisulfite sequencing of the H9 cell line; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Thomson Laboratory", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "H9", "LINEAGE": "NA", "DIFFERENTIATION_STAGE": "embryonic stem cell", "DIFFERENTIATION_METHOD": "NA", "PASSAGE": "42", "MEDIUM": "TeSR", "sex": "female", "BATCH": "Replicate 1", "sample_term_id": "NTR_0000838"}
SRX056695 ESC
0.824
12.2
38747
1108.8
3953
8852.2
4079
10839.5
0.987
title: Whole genome shotgun bisulfite sequencing of the H9 cell line; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Thomson Laboratory", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "H9", "LINEAGE": "NA", "DIFFERENTIATION_STAGE": "embryonic stem cell", "DIFFERENTIATION_METHOD": "NA", "PASSAGE": "40", "MEDIUM": "TeSR", "sex": "female", "BATCH": "Replicate 2", "sample_term_id": "NTR_0000838"}
SRX101206 ESC
0.840
8.6
33680
1236.0
1221
17208.1
2091
14903.7
0.991
title: Whole genome shotgun bisulfite sequencing of the H1 mesendoderm cell line; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Thomson Laboratory", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "H1", "LINEAGE": "NA", "DIFFERENTIATION_STAGE": "embryonic stem cell differentiated into mesendoderm cells", "DIFFERENTIATION_METHOD": "H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium", "PASSAGE": "20", "MEDIUM": "TeSR", "sex": "male", "BATCH": "Replicate 1", "sample_term_id": "NTR_0000856"}
SRX101207 ESC
0.841
10.7
35539
1180.0
1901
16736.7
4208
8150.7
0.991
title: Whole genome shotgun bisulfite sequencing of the H1 mesendoderm cell line; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Thomson Laboratory", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "H1", "LINEAGE": "NA", "DIFFERENTIATION_STAGE": "embryonic stem cell differentiated into mesendoderm cells", "DIFFERENTIATION_METHOD": "H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium", "PASSAGE": "20", "MEDIUM": "TeSR", "sex": "male", "BATCH": "Replicate 1", "sample_term_id": "NTR_0000856"}
SRX101208 ESC
0.838
8.9
34676
1211.1
1448
7839.2
1957
14850.3
0.991
title: Whole genome shotgun bisulfite sequencing of the H1 mesendoderm cell line; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Thomson Laboratory", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "H1", "LINEAGE": "NA", "DIFFERENTIATION_STAGE": "embryonic stem cell differentiated into mesendoderm cells", "DIFFERENTIATION_METHOD": "H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium", "PASSAGE": "20", "MEDIUM": "TeSR", "sex": "male", "BATCH": "Replicate 2", "sample_term_id": "NTR_0000856"}
SRX101209 ESC
0.838
2.2
25692
1602.0
80
2005.8
579
33269.0
0.992
title: Whole genome shotgun bisulfite sequencing of the H1 mesendoderm cell line; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Thomson Laboratory", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "H1", "LINEAGE": "NA", "DIFFERENTIATION_STAGE": "embryonic stem cell differentiated into mesendoderm cells", "DIFFERENTIATION_METHOD": "H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium", "PASSAGE": "20", "MEDIUM": "TeSR", "sex": "male", "BATCH": "Replicate 2", "sample_term_id": "NTR_0000856"}
SRX116603 ESC
0.789
30.7
50253
949.0
56554
2915.5
4070
37507.0
0.994
title: Whole genome shotgun bisulfite sequencing of mesenchymal cells derived from H1 embryonic stem cells; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Thomson Laboratory", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "H1", "LINEAGE": "NA", "DIFFERENTIATION_STAGE": "embryonic stem cell differentiated by treatment with fibronectin and human collagen", "DIFFERENTIATION_METHOD": "H1 cells were cultured on plates coated with fibronectin and human collagen", "PASSAGE": "5", "MEDIUM": "50% StemLine II serum-free HSC expansion medium (HSFEM; Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2.", "sex": "male", "BATCH": "Replicate 1", "sample_term_id": "EFO_0000586"}
SRX116604 ESC
0.779
15.5
41662
1050.2
18625
4814.6
1957
216307.5
0.993
title: Whole genome shotgun bisulfite sequencing of mesenchymal cells derived from H1 embryonic stem cells; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Thomson Laboratory", "BIOMATERIAL_TYPE": "Cell Line", "LINE": "H1", "LINEAGE": "NA", "DIFFERENTIATION_STAGE": "embryonic stem cell differentiated by treatment with fibronectin and human collagen", "DIFFERENTIATION_METHOD": "H1 cells were cultured on plates coated with fibronectin and human collagen", "PASSAGE": "5", "MEDIUM": "50% StemLine II serum-free HSC expansion medium (HSFEM; Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2.", "sex": "male", "BATCH": "Replicate 2", "sample_term_id": "EFO_0000586"}
SRX175348 Sigmoid Colon
0.799
64.2
49650
1101.5
203815
3389.4
3775
11645.6
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Sigmoid Colon Cells from Human STL001; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Sigmoid Colon", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL001", "DONOR_AGE": "3", "DONOR_HEALTH_STATUS": "healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian and African American", "sample_term_id": "UBERON_0001159"}
SRX175349 Small Intestine
0.775
58.7
49125
1094.0
209886
3456.5
3279
11959.7
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Small Bowel Cells from Human STL001; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Small Intestine", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL001", "DONOR_AGE": "3", "DONOR_HEALTH_STATUS": "healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian and African American", "sample_term_id": "UBERON_0002108"}
SRX175350 Lung
0.792
59.7
55202
1215.8
215901
3253.3
3376
18035.0
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Lung Cells from Human STL002; {"MOLECULE": "genomic DNA", "disease": "iron deficiency, bipolar", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Lung", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL002", "DONOR_AGE": "30", "DONOR_HEALTH_STATUS": "iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "female", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0002048"}
SRX175351 Aorta
0.771
64.4
88021
1122.7
135196
2775.5
3399
16054.9
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Aorta Cells from Human STL003; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Aorta", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL003", "DONOR_AGE": "34", "DONOR_HEALTH_STATUS": "polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0000947"}
SRX175352 Esophagus
0.776
61.7
59436
1250.3
213125
3458.3
3144
12551.8
0.996
title: Whole Genome Shotgun Bisulfite Sequencing of Esophagus Cells from Human STL003; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Esophagus", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL003", "DONOR_AGE": "34", "DONOR_HEALTH_STATUS": "polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0001043"}
SRX175353 Left Ventricle
0.778
62.1
61971
1166.2
206742
3327.5
3065
18790.4
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Left Ventricle Cells from Human STL003; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Left Ventricle", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL003", "DONOR_AGE": "34", "DONOR_HEALTH_STATUS": "polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0002084"}
SRX175354 Pancreas
0.704
60.1
64996
1696.6
237450
4971.4
2145
431169.8
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Pancreas Cells from Human STL003; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Pancreas", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL003", "DONOR_AGE": "34", "DONOR_HEALTH_STATUS": "polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0001264"}
SRX175355 Spleen
0.779
59.6
60938
1000.8
211231
3307.4
3205
11014.2
0.996
title: Whole Genome Shotgun Bisulfite Sequencing of Spleen Cells from Human STL003; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Spleen", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL003", "DONOR_AGE": "34", "DONOR_HEALTH_STATUS": "polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0002106"}
SRX190150 Left Ventricle
0.800
39.6
57850
1121.0
130182
3093.1
3330
20275.2
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Left Ventricle Cells from Human STL001; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Left Ventricle", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL001", "DONOR_AGE": "3", "DONOR_HEALTH_STATUS": "healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian and African American", "sample_term_id": "UBERON_0002084"}
SRX190151 Thymus
0.861
48.3
61605
1036.4
59241
2223.9
4092
14917.8
0.996
title: Whole Genome Shotgun Bisulfite Sequencing of Thymus Cells from Human STL001; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Thymus", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL001", "DONOR_AGE": "3", "DONOR_HEALTH_STATUS": "healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "Male", "DONOR_ETHNICITY": "Caucasian and African American", "sample_term_id": "UBERON_0002370"}
SRX190152 Ovary
0.764
46.4
90613
1231.4
86943
2520.7
2843
20837.3
0.996
title: Whole Genome Shotgun Bisulfite Sequencing of Ovary Cells from Human STL002; {"MOLECULE": "genomic DNA", "disease": "iron deficiency, bipolar", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Ovary", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL002", "DONOR_AGE": "30", "DONOR_HEALTH_STATUS": "iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "Female", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0000992"}
SRX190153 Adrenal Gland
0.775
31.3
49107
1041.5
113412
2902.0
2604
16306.6
0.996
title: Whole Genome Shotgun Bisulfite Sequencing of Adrenal Cells from Human STL003; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Adrenal Gland", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL003", "DONOR_AGE": "34", "DONOR_HEALTH_STATUS": "polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0002369"}
SRX190155 Adipose Tissue
0.803
33.6
54956
1071.4
118687
2902.6
3154
13709.8
0.996
title: Whole Genome Shotgun Bisulfite Sequencing of Fat Cells from Human STL003; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Adipose Tissue", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL003", "DONOR_AGE": "34", "DONOR_HEALTH_STATUS": "polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0001013"}
SRX190156 Gastric
0.784
38.8
68083
1256.6
143263
2950.7
3388
12814.5
0.996
title: Whole Genome Shotgun Bisulfite Sequencing of Gastric Cells from Human STL003; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Gastric", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL003", "DONOR_AGE": "34", "DONOR_HEALTH_STATUS": "polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0000945"}
SRX190158 Psoas Muscle
0.770
51.0
76888
1269.3
160119
3116.0
3135
16422.9
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Psoas Cells from Human STL003; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Psoas Muscle", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL003", "DONOR_AGE": "34", "DONOR_HEALTH_STATUS": "polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0008450"}
SRX190159 Right Atrium
0.782
42.1
63269
1134.4
156447
3127.4
2786
17601.3
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Right Atrium Cells from Human STL003; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Right Atrium", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL003", "DONOR_AGE": "34", "DONOR_HEALTH_STATUS": "polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0002078"}
SRX190160 Right Ventricle
0.787
34.3
57324
1096.6
124253
2982.2
3049
17884.9
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Right Ventricle Cells from Human STL003; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Right Ventricle", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL003", "DONOR_AGE": "34", "DONOR_HEALTH_STATUS": "polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0002080"}
SRX190161 Sigmoid Colon
0.771
58.3
79452
1229.1
167111
3081.1
3105
12864.6
0.996
title: Whole Genome Shotgun Bisulfite Sequencing of Sigmoid Colon Cells from Human STL003; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Sigmoid Colon", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL003", "DONOR_AGE": "34", "DONOR_HEALTH_STATUS": "polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0001159"}
SRX213279 Bladder
0.793
51.7
67088
1197.0
154387
3011.6
2980
16710.5
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Bladder Cells from Human STL001; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Bladder", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL001", "DONOR_AGE": "3", "DONOR_HEALTH_STATUS": "healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "Male", "DONOR_ETHNICITY": "Caucasian and African American", "sample_term_id": "UBERON_0001255"}
SRX213280 Liver
0.786
52.6
57709
1266.2
177055
3192.1
3072
219045.1
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Liver Cells from Human STL011; {"MOLECULE": "genomic DNA", "disease": "coronary artery disease", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Liver", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL011", "DONOR_AGE": "32", "DONOR_HEALTH_STATUS": "coronary artery disease. No history of hypertension or diabetes.", "sex": "Male", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0002107"}
SRX213911 Right Ventricle
0.792
7.8
40664
1225.3
5546
11827.5
1594
28885.7
0.994
title: Whole Genome Shotgun Bisulfite Sequencing of Right Ventricle Cells from Human STL003; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Right Ventricle", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL003", "DONOR_AGE": "34", "DONOR_HEALTH_STATUS": "polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0002080"}
SRX263874 Bladder
0.793
4.0
36286
1444.8
279
66566.4
1190
31939.8
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Bladder Cells from Human STL001; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Bladder", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL001", "DONOR_AGE": "3", "DONOR_HEALTH_STATUS": "healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "Male", "DONOR_ETHNICITY": "Caucasian and African American", "sample_term_id": "UBERON_0001255"}
SRX263875 Left Ventricle
0.798
8.7
41073
1204.4
8362
3872.0
2692
20045.3
0.994
title: Whole Genome Shotgun Bisulfite Sequencing of Left Ventricle Cells from Human STL001; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Left Ventricle", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL001", "DONOR_AGE": "3", "DONOR_HEALTH_STATUS": "healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian and African American", "sample_term_id": "UBERON_0002084"}
SRX263876 Left Ventricle
0.796
4.2
35472
1425.5
419
44930.6
1129
47673.1
0.994
title: Whole Genome Shotgun Bisulfite Sequencing of Left Ventricle Cells from Human STL001; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Left Ventricle", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL001", "DONOR_AGE": "3", "DONOR_HEALTH_STATUS": "healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian and African American", "sample_term_id": "UBERON_0002084"}
SRX263877 Small Intestine
0.791
4.4
32034
1456.2
632
1740.0
1153
23859.4
0.996
title: Whole Genome Shotgun Bisulfite Sequencing of Small Bowel Cells from Human STL001; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Small Intestine", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL001", "DONOR_AGE": "3", "DONOR_HEALTH_STATUS": "healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian and African American", "sample_term_id": "UBERON_0002108"}
SRX263878 Thymus
0.861
3.8
37579
1266.6
225
2270.0
1278
31893.0
0.996
title: Whole Genome Shotgun Bisulfite Sequencing of Thymus Cells from Human STL001; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Thymus", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL001", "DONOR_AGE": "3", "DONOR_HEALTH_STATUS": "healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "Male", "DONOR_ETHNICITY": "Caucasian and African American", "sample_term_id": "UBERON_0002370"}
SRX263879 Ovary
0.759
3.8
46399
1544.9
234
79462.4
988
37623.1
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Ovary Cells from Human STL002; {"MOLECULE": "genomic DNA", "disease": "iron deficiency, bipolar", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Ovary", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL002", "DONOR_AGE": "30", "DONOR_HEALTH_STATUS": "iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "Female", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0000992"}
SRX263880 Adrenal Gland
0.772
8.2
35306
1270.9
5089
6902.8
2350
14035.6
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Adrenal Cells from Human STL003; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Adrenal Gland", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL003", "DONOR_AGE": "34", "DONOR_HEALTH_STATUS": "polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0002369"}
SRX263881 Adrenal Gland
0.771
8.1
35454
1265.4
5057
6909.3
2614
13502.2
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Adrenal Cells from Human STL003; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Adrenal Gland", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL003", "DONOR_AGE": "34", "DONOR_HEALTH_STATUS": "polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0002369"}
SRX263882 Aorta
0.787
9.4
60961
1161.2
2641
12198.6
2931
14109.4
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Aorta Cells from Human STL003; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Aorta", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL003", "DONOR_AGE": "34", "DONOR_HEALTH_STATUS": "polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0000947"}
SRX263883 Aorta
0.786
9.7
61530
1154.4
2908
18434.9
2644
15218.1
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Aorta Cells from Human STL003; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Aorta", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL003", "DONOR_AGE": "34", "DONOR_HEALTH_STATUS": "polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0000947"}
SRX263884 Aorta
0.787
9.5
60939
1170.7
2650
11818.3
2796
14688.4
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Aorta Cells from Human STL003; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Aorta", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL003", "DONOR_AGE": "34", "DONOR_HEALTH_STATUS": "polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0000947"}
SRX263885 Aorta
0.783
9.2
59811
1173.2
2443
12699.6
2630
14868.3
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Aorta Cells from Human STL003; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Aorta", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL003", "DONOR_AGE": "34", "DONOR_HEALTH_STATUS": "polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0000947"}
SRX263886 Adipose Tissue
0.798
8.8
37726
1223.6
8990
3841.7
2450
13084.7
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Fat Cells from Human STL003; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Adipose Tissue", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL003", "DONOR_AGE": "34", "DONOR_HEALTH_STATUS": "polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0001013"}
SRX263887 Adipose Tissue
0.806
8.9
39018
1194.4
9948
6515.0
2821
12078.3
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Fat Cells from Human STL003; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Adipose Tissue", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL003", "DONOR_AGE": "34", "DONOR_HEALTH_STATUS": "polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0001013"}
SRX263888 Gastric
0.792
4.3
39344
1499.0
453
2055.9
1169
24935.7
0.996
title: Whole Genome Shotgun Bisulfite Sequencing of Gastric Cells from Human STL003; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Gastric", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL003", "DONOR_AGE": "34", "DONOR_HEALTH_STATUS": "polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0000945"}
SRX263889 Gastric
0.793
8.3
46403
1302.2
5963
4800.7
2818
11459.3
0.996
title: Whole Genome Shotgun Bisulfite Sequencing of Gastric Cells from Human STL003; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Gastric", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL003", "DONOR_AGE": "34", "DONOR_HEALTH_STATUS": "polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0000945"}
SRX263890 Right Atrium
0.784
4.6
36518
1423.1
631
30411.8
1057
37683.4
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Right Atrium Cells from Human STL003; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Right Atrium", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL003", "DONOR_AGE": "34", "DONOR_HEALTH_STATUS": "polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0002078"}
SRX263891 Right Atrium
0.784
4.5
36789
1416.5
552
49493.1
1122
35612.1
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Right Atrium Cells from Human STL003; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Right Atrium", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL003", "DONOR_AGE": "34", "DONOR_HEALTH_STATUS": "polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0002078"}
SRX263892 Right Ventricle
0.783
4.3
34743
1465.9
481
56413.8
1154
40920.2
0.994
title: Whole Genome Shotgun Bisulfite Sequencing of Right Ventricle Cells from Human STL003; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Right Ventricle", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL003", "DONOR_AGE": "34", "DONOR_HEALTH_STATUS": "polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0002080"}
SRX263893 Right Ventricle
0.795
8.8
41302
1210.9
8745
3825.6
2675
16364.7
0.994
title: Whole Genome Shotgun Bisulfite Sequencing of Right Ventricle Cells from Human STL003; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Right Ventricle", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL003", "DONOR_AGE": "34", "DONOR_HEALTH_STATUS": "polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0002080"}
SRX388732 Adipose
0.770
21.9
49251
1140.1
54361
3244.2
2512
23182.5
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Fat Cells from Human STL001; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Adipose", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL001", "DONOR_AGE": "3", "DONOR_HEALTH_STATUS": "healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "Male", "DONOR_ETHNICITY": "Caucasian and African American", "sample_term_id": "UBERON_0001013"}
SRX388733 Gastric
0.794
25.7
48865
1127.6
95875
2577.8
3108
13753.8
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Gastric Cells from Human STL001; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Gastric", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL001", "DONOR_AGE": "3", "DONOR_HEALTH_STATUS": "healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "Male", "DONOR_ETHNICITY": "Caucasian and African American", "sample_term_id": "UBERON_0000945"}
SRX388734 Lung
0.831
23.2
59979
1021.8
55463
3002.5
3562
13809.2
0.996
title: Whole Genome Shotgun Bisulfite Sequencing of Lung Cells from Human STL001; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Lung", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL001", "DONOR_AGE": "3", "DONOR_HEALTH_STATUS": "healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "Male", "DONOR_ETHNICITY": "Caucasian and African American", "sample_term_id": "UBERON_0002048"}
SRX388735 Psoas Muscle
0.799
22.7
55970
1096.5
59618
3038.7
2934
17399.7
0.993
title: Whole Genome Shotgun Bisulfite Sequencing of Psoas Cells from Human STL001; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Psoas Muscle", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL001", "DONOR_AGE": "3", "DONOR_HEALTH_STATUS": "healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "Male", "DONOR_ETHNICITY": "Caucasian and African American", "sample_term_id": "UBERON_0008450"}
SRX388736 Right Ventricle
0.804
25.6
56927
1088.7
76146
2961.0
3072
21377.4
0.994
title: Whole Genome Shotgun Bisulfite Sequencing of Right Ventricle Cells from Human STL001; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Right Ventricle", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL001", "DONOR_AGE": "3", "DONOR_HEALTH_STATUS": "healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "Male", "DONOR_ETHNICITY": "Caucasian and African American", "sample_term_id": "UBERON_0002080"}
SRX388737 Spleen
0.835
25.5
54463
1012.7
62913
2469.6
3425
13472.2
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Spleen Cells from Human STL001; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Spleen", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL001", "DONOR_AGE": "3", "DONOR_HEALTH_STATUS": "healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "Male", "DONOR_ETHNICITY": "Caucasian and African American", "sample_term_id": "UBERON_0002106"}
SRX388738 Adrenal Gland
0.791
26.2
50513
1114.7
86571
2507.9
3639
18516.1
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Adrenal Cells from Human STL002; {"MOLECULE": "genomic DNA", "disease": "iron deficiency, bipolar", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Adrenal Gland", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL002", "DONOR_AGE": "30", "DONOR_HEALTH_STATUS": "iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "Female", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0002369"}
SRX388739 Aorta
0.779
22.9
85261
1080.1
19921
3191.1
2992
17968.3
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Aorta Cells from Human STL002; {"MOLECULE": "genomic DNA", "disease": "iron deficiency, bipolar", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Aorta", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL002", "DONOR_AGE": "30", "DONOR_HEALTH_STATUS": "iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "Female", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0000947"}
SRX388740 Esophagus
0.786
23.3
42454
1172.1
88863
2622.2
2711
15843.0
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Esophagus Cells from Human STL002; {"MOLECULE": "genomic DNA", "disease": "iron deficiency, bipolar", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Esophagus", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL002", "DONOR_AGE": "30", "DONOR_HEALTH_STATUS": "iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "Female", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0001043"}
SRX388741 Adipose
0.800
24.5
51616
1119.5
89980
2569.8
3298
15638.1
0.996
title: Whole Genome Shotgun Bisulfite Sequencing of Fat Cells from Human STL002; {"MOLECULE": "genomic DNA", "disease": "iron deficiency, bipolar", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Adipose", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL002", "DONOR_AGE": "30", "DONOR_HEALTH_STATUS": "iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "Female", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0001013"}
SRX388742 Gastric
0.781
27.1
64556
1266.4
91296
2583.2
3045
16659.3
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Gastric Cells from Human STL002; {"MOLECULE": "genomic DNA", "disease": "iron deficiency, bipolar", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Gastric", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL002", "DONOR_AGE": "30", "DONOR_HEALTH_STATUS": "iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "Female", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0000945"}
SRX388743 Pancreas
0.759
23.3
56250
1290.4
52123
2740.8
3087
196824.5
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Pancreas Cells from Human STL002; {"MOLECULE": "genomic DNA", "disease": "iron deficiency, bipolar", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Pancreas", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL002", "DONOR_AGE": "30", "DONOR_HEALTH_STATUS": "iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "Female", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0001264"}
SRX388744 Psoas Muscle
0.779
23.4
68187
1205.7
64355
2562.3
2988
19298.2
0.994
title: Whole Genome Shotgun Bisulfite Sequencing of Psoas Cells from Human STL002; {"MOLECULE": "genomic DNA", "disease": "iron deficiency, bipolar", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Psoas Muscle", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL002", "DONOR_AGE": "30", "DONOR_HEALTH_STATUS": "iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "Female", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0008450"}
SRX388745 Small Intestine
0.771
20.8
49598
1271.8
70257
2563.7
2756
13286.1
0.996
title: Whole Genome Shotgun Bisulfite Sequencing of Small Bowel Cells from Human STL002; {"MOLECULE": "genomic DNA", "disease": "iron deficiency, bipolar", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Small Intestine", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL002", "DONOR_AGE": "30", "DONOR_HEALTH_STATUS": "iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "Female", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0002108"}
SRX388746 Spleen
0.804
27.6
53921
1060.3
88064
2512.6
3218
15663.0
0.995
title: Whole Genome Shotgun Bisulfite Sequencing of Spleen Cells from Human STL002; {"MOLECULE": "genomic DNA", "disease": "iron deficiency, bipolar", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Spleen", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL002", "DONOR_AGE": "30", "DONOR_HEALTH_STATUS": "iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "Female", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0002106"}
SRX388747 Small Intestine
0.775
21.7
71460
1190.3
35742
2139.3
3156
12325.0
0.996
title: Whole Genome Shotgun Bisulfite Sequencing of Small Bowel Cells from Human STL003; {"MOLECULE": "genomic DNA", "disease": "None", "biomaterial_provider": "Shin Lin, Stanford University", "BIOMATERIAL_TYPE": "Primary Tissue", "tissue": "Small Intestine", "TISSUE_DEPOT": "N/A", "collection_method": "Autopsy", "DONOR_ID": "STL003", "DONOR_AGE": "34", "DONOR_HEALTH_STATUS": "polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)", "sex": "male", "DONOR_ETHNICITY": "Caucasian", "sample_term_id": "UBERON_0002108"}
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
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 .
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