Induced pluripotent stem cells.

Description

This samples serie was produced as part of the RoadMap Project.

Source

Files downloaded from GEO FTP server: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/roadmapepigenomics/by_sample/
Input file format: BED

Samples

From Human Feb. 2009 (GRCh37/hg19) Assembly.

ChIP-seq data:

Filename Description Feature GEO-ID
1 GSM752979_UCSD.iPS_DF_19.11.H3K4me1.SK473.sga iPS DF 19|11|rep 10 H3K4me1 GSM752979
2 GSM706074_UCSD.iPS_DF_19.11.H3K4me3.SK227.sga iPS DF 19|11|rep 11 H3K4me3 GSM706074
3 GSM752984_UCSD.iPS_DF_19.11.H3K4me3.SK475.sga iPS DF 19|11|rep 12 H3K4me3 GSM752984
4 GSM706079_UCSD.iPS_DF_19.11.H3K9me3.SK232.sga iPS DF 19|11|rep 13 H3K9me3 GSM706079
5 GSM752988_UCSD.iPS_DF_19.11.H3K9me3.SK474.sga iPS DF 19|11|rep 14 H3K9me3 GSM752988
6 GSM706082_UCSD.iPS_DF_19.11.Input.SKiPS19.11-1.sga iPS DF 19|11|rep 15 Input GSM706082
7 GSM752992_UCSD.iPS_DF_19.11.Input.SK446.sga iPS DF 19|11|rep 16 Input GSM752992
8 GSM706065_UCSD.iPS_DF_19.11.H3K27ac.SK402.sga iPS DF 19|11|rep 3 H3K27ac GSM706065
9 GSM752965_UCSD.iPS_DF_19.11.H3K27ac.SK395.sga iPS DF 19|11|rep 4 H3K27ac GSM752965
10 GSM752966_UCSD.iPS_DF_19.11.H3K27ac.SK434.sga iPS DF 19|11|rep 5 H3K27ac GSM752966
11 GSM706067_UCSD.iPS_DF_19.11.H3K27me3.SK230.sga iPS DF 19|11|rep 6 H3K27me3 GSM706067
12 GSM752970_UCSD.iPS_DF_19.11.H3K27me3.SK435.sga iPS DF 19|11|rep 7 H3K27me3 GSM752970
13 GSM752974_UCSD.iPS_DF_19.11.H3K36me3.SK472.sga iPS DF 19|11|rep 8 H3K36me3 GSM752974
14 GSM706072_UCSD.iPS_DF_19.11.H3K4me1.SK401.sga iPS DF 19|11|rep 9 H3K4me1 GSM706072
15 GSM752985_UCSD.iPS_DF_6.9.H3K4me3.SK471.sga iPS DF 6|9|rep 10 H3K4me3 GSM752985
16 GSM706080_UCSD.iPS_DF_6.9.H3K9me3.SK274.sga iPS DF 6|9|rep 11 H3K9me3 GSM706080
17 GSM752989_UCSD.iPS_DF_6.9.H3K9me3.SK503.sga iPS DF 6|9|rep 12 H3K9me3 GSM752989
18 GSM706083_UCSD.iPS_DF_6.9.Input.SKiPS6.9-1.sga iPS DF 6|9|rep 13 Input GSM706083
19 GSM752993_UCSD.iPS_DF_6.9.Input.SK445.sga iPS DF 6|9|rep 14 Input GSM752993
20 GSM752967_UCSD.iPS_DF_6.9.H3K27ac.SK432.sga iPS DF 6|9|rep 2 H3K27ac GSM752967
21 GSM706068_UCSD.iPS_DF_6.9.H3K27me3.SK275.sga iPS DF 6|9|rep 3 H3K27me3 GSM706068
22 GSM752971_UCSD.iPS_DF_6.9.H3K27me3.SK433.sga iPS DF 6|9|rep 4 H3K27me3 GSM752971
23 GSM706070_UCSD.iPS_DF_6.9.H3K36me3.SK400.sga iPS DF 6|9|rep 5 H3K36me3 GSM706070
24 GSM752975_UCSD.iPS_DF_6.9.H3K36me3.SK468.sga iPS DF 6|9|rep 6 H3K36me3 GSM752975
25 GSM706073_UCSD.iPS_DF_6.9.H3K4me1.SK397.sga iPS DF 6|9|rep 7 H3K4me1 GSM706073
26 GSM752980_UCSD.iPS_DF_6.9.H3K4me1.SK469.sga iPS DF 6|9|rep 8 H3K4me1 GSM752980
27 GSM706075_UCSD.iPS_DF_6.9.H3K4me3.SK398.sga iPS DF 6|9|rep 9 H3K4me3 GSM706075
28 GSM537694_BI.iPS-11a.H3K4me3.Solexa-11733.sga iPS-11a|H3K4me3 H3K4me3 GSM537694
29 GSM537693_BI.iPS-11a.Input.Solexa-11734.sga iPS-11a|Input WCE GSM537693
30 GSM621433_BI.iPS-15b.H3K27me3.Lib_MC_20100128_05--ChIP_MC_20100125_05_hiPS-15b_H3K27Me3.sga iPS-15b|H3K27me3 H3K27me3 GSM621433
31 GSM537690_BI.iPS-15b.H3K36me3.Solexa-20749.sga iPS-15b|H3K36me3 H3K36me3 GSM537690
32 GSM772767_BI.iPS-15b.H3K4me1.Lib_MC_20100211_04--ChIP_MC_20100208_04_hiPS-15b_H3K4Me1.sga iPS-15b|H3K4me1 H3K4me1 GSM772767
33 GSM537687_BI.iPS-15b.H3K4me3.Solexa-20743.sga iPS-15b|H3K4me3 H3K4me3 GSM537687
34 GSM537692_BI.iPS-15b.H3K9ac.Solexa-20747.sga iPS-15b|H3K9ac H3K9ac GSM537692
35 GSM537691_BI.iPS-15b.H3K9me3.Solexa-20732.sga iPS-15b|H3K9me3 H3K9me3 GSM537691
36 GSM537696_BI.iPS-15b.Input.Solexa-15157.sga iPS-15b|Input|rep 1 WCE GSM537696
37 GSM621444_BI.iPS-15b.Input.Lib_MC_20100128_06--ChIP_MC_20100125_06_hiPS-15b_WCE.sga iPS-15b|Input|rep 2 WCE GSM621444
38 GSM773033_BI.iPS-18a.H3K27ac.DNA_Lib_349.sga iPS-18a|H3K27ac H3K27ac GSM773033
39 GSM772935_BI.iPS-18a.H3K27me3.DNA_Lib_348.sga iPS-18a|H3K27me3 H3K27me3 GSM772935
40 GSM773027_BI.iPS-18a.H3K36me3.DNA_Lib_347.sga iPS-18a|H3K36me3 H3K36me3 GSM773027
41 GSM773028_BI.iPS-18a.H3K4me1.DNA_Lib_346.sga iPS-18a|H3K4me1 H3K4me1 GSM773028
42 GSM773029_BI.iPS-18a.H3K4me3.DNA_Lib_345.sga iPS-18a|H3K4me3 H3K4me3 GSM773029
43 GSM773030_BI.iPS-18a.H3K9ac.DNA_Lib_344.sga iPS-18a|H3K9ac H3K9ac GSM773030
44 GSM773023_BI.iPS-18a.H3K9me3.DNA_Lib_343.sga iPS-18a|H3K9me3 H3K9me3 GSM773023
45 GSM773024_BI.iPS-18a.Input.DNA_Lib_342.sga iPS-18a|Input WCE GSM773024
46 GSM621411_BI.iPS-18b.Input.Lib_MC_20090720_02--ChIP_MC_20090715_02_hiPS-18b_WCE.sga iPS-18b|Input WCE GSM621411
47 GSM537674_BI.iPS-18c.H3K27me3.Solexa-19791.sga iPS-18c|H3K27me3 H3K27me3 GSM537674
48 GSM537675_BI.iPS-18c.H3K36me3.Solexa-19808.sga iPS-18c|H3K36me3 H3K36me3 GSM537675
49 GSM537671_BI.iPS-18c.H3K4me3.Solexa-15173.sga iPS-18c|H3K4me3|rep 1 H3K4me3 GSM537671
50 GSM537676_BI.iPS-18c.H3K4me3.Solexa-19747.sga iPS-18c|H3K4me3|rep 2 H3K4me3 GSM537676
51 GSM537677_BI.iPS-18c.H3K9ac.Solexa-19756.sga iPS-18c|H3K9ac H3K9ac GSM537677
52 GSM537678_BI.iPS-18c.H3K9me3.Solexa-19774.sga iPS-18c|H3K9me3 H3K9me3 GSM537678
53 GSM621407_BI.iPS-18c.Input.Lib_MC_20100108_07--ChIP_MC_20100105_07_hiPS-18c_WCE.sga iPS-18c|Input WCE GSM621407
54 GSM772848_BI.iPS-20b.H3K27ac.DNA_Lib_357.sga iPS-20b|H3K27ac H3K27ac GSM772848
55 GSM537700_BI.iPS-20b.H3K27me3.Solexa-15159.sga iPS-20b|H3K27me3|rep 1 H3K27me3 GSM537700
56 GSM621416_BI.iPS-20b.H3K27me3.Lib_MC_20100119_06--ChIP_MC_20100113_06_hiPS-20b_H3K27Me3.sga iPS-20b|H3K27me3|rep 2 H3K27me3 GSM621416
57 GSM772847_BI.iPS-20b.H3K27me3.DNA_Lib_356.sga iPS-20b|H3K27me3|rep 3 H3K27me3 GSM772847
58 GSM537704_BI.iPS-20b.H3K36me3.Solexa-20763.sga iPS-20b|H3K36me3|rep 1 H3K36me3 GSM537704
59 GSM772846_BI.iPS-20b.H3K36me3.DNA_Lib_355.sga iPS-20b|H3K36me3|rep 2 H3K36me3 GSM772846
60 GSM772804_BI.iPS-20b.H3K4me1.Lib_MC_20100211_03--ChIP_MC_20100208_03_hiPS-20b_H3K4Me1.sga iPS-20b|H3K4me1|rep 1 H3K4me1 GSM772804
61 GSM772845_BI.iPS-20b.H3K4me1.DNA_Lib_354.sga iPS-20b|H3K4me1|rep 2 H3K4me1 GSM772845
62 GSM621423_BI.iPS-20b.H3K4me3.Lib_MC_20100119_05--ChIP_MC_20100113_05_hiPS-20b_H3K4Me3.sga iPS-20b|H3K4me3|rep 1 H3K4me3 GSM621423
63 GSM772844_BI.iPS-20b.H3K4me3.DNA_Lib_353.sga iPS-20b|H3K4me3|rep 2 H3K4me3 GSM772844
64 GSM537689_BI.iPS-20b.H3K9ac.Solexa-20764.sga iPS-20b|H3K9ac|rep 1 H3K9ac GSM537689
65 GSM772843_BI.iPS-20b.H3K9ac.DNA_Lib_352.sga iPS-20b|H3K9ac|rep 2 H3K9ac GSM772843
66 GSM537688_BI.iPS-20b.H3K9me3.Solexa-20765.sga iPS-20b|H3K9me3|rep 1 H3K9me3 GSM537688
67 GSM772842_BI.iPS-20b.H3K9me3.DNA_Lib_351.sga iPS-20b|H3K9me3|rep 2 H3K9me3 GSM772842
68 GSM537701_BI.iPS-20b.Input.Solexa-10232.sga iPS-20b|Input|rep 1 WCE GSM537701
69 GSM621412_BI.iPS-20b.Input.Lib_MC_20100119_07--ChIP_MC_20100113_07_hiPS-20b_WCE.sga iPS-20b|Input|rep 2 WCE GSM621412
70 GSM772841_BI.iPS-20b.Input.DNA_Lib_350.sga iPS-20b|Input|rep 3 WCE GSM772841
71 GSM772863_BI.iPS-20b.Input.DNA_Lib_440.sga iPS-20b|Input|rep 4 WCE GSM772863
72 GSM706069.sga sga| H3K36me3 GSM706069

DNase FAIRE data:

Filename Description Feature GEO-ID
1 GSM909311_UW.iPS_DF_19.11.Digital_Genomic_Footprinting.DGF.DS15153.sga iPS DF 19|11|rep 1 DNase-HS GSM909311
2 GSM665801_UW.iPS_DF_19.11.ChromatinAccessibility.DS15153.sga iPS DF 19|11|rep 2 DNase-seq GSM665801
3 GSM665800_UW.iPS_DF_19.7.ChromatinAccessibility.DS15148.sga iPS DF 19|7 DNase-seq GSM665800
4 GSM665803_UW.iPS_DF_4.7.ChromatinAccessibility.DS15169.sga iPS DF 4|7 DNase-seq GSM665803
5 GSM665802_UW.iPS_DF_6.9.ChromatinAccessibility.DS15164.sga iPS DF 6|9|rep 1 DNase-seq GSM665802

Technical Notes

BED files were downloaded from the FTP and converted in SGA format using bed2sga (ChIP-seq).

References

Genome browser viewable files