ChIP-seq and DNase-seq for Fetal Brain and fetal spinal cord tissues

Description

These sample series were produced as part of the RoadMap Project. This project has generated high-quality genome-wide maps of several key histone modifications, chromatin accessibility, DNA methylation and mRNA expression across 100s of human stem cells and primary ex vivo tissues selected to represent the normal counterparts of tissues and organ systems frequently involved in human disease.

Experiments: ChIP-seq against H3K27me3, H3K4me1, H3K36me3; H3K4me3, H3K9ac and H3K9me3; Chromatin accessibility determination via DNase-seq, in human fetal brain, and fetal spinal cord tissues. Samples for the input control are taken from the whole cell extract (WCE).

Source

Samples

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

ChIP-seq data:

Filename Description Feature GEO-ID
1 GSM621393_BI.Fetal_Brain.H3K27me3.UW_H-22510.sga Fetal Brain|H3K27me3|rep 1 H3K27me3 GSM621393
2 GSM669625_UCSF-UBC.Fetal_Brain.H3K27me3.HuFNSC-T.sga Fetal Brain|H3K27me3|rep 2 H3K27me3 GSM669625
3 GSM806937_UCSF-UBC.Fetal_Brain.H3K27me3.HuFNSC02.sga Fetal Brain|H3K27me3|rep 3 H3K27me3 GSM806937
4 GSM806945_UCSF-UBC.Fetal_Brain.H3K27me3.HuFNSC01.sga Fetal Brain|H3K27me3|rep 4 H3K27me3 GSM806945
5 GSM916061_BI.Fetal_Brain.H3K27me3.UW_H22676.sga Fetal Brain|H3K27me3|rep 5 H3K27me3 GSM916061
6 GSM621410_BI.Fetal_Brain.H3K36me3.UW_H-22510.sga Fetal Brain|H3K36me3|rep 1 H3K36me3 GSM621410
7 GSM806938_UCSF-UBC.Fetal_Brain.H3K36me3.HuFNSC02.sga Fetal Brain|H3K36me3|rep 2 H3K36me3 GSM806938
8 GSM806946_UCSF-UBC.Fetal_Brain.H3K36me3.HuFNSC01.sga Fetal Brain|H3K36me3|rep 3 H3K36me3 GSM806946
9 GSM706850_BI.Fetal_Brain.H3K4me1.UW_H22676.sga Fetal Brain|H3K4me1|rep 1 H3K4me1 GSM706850
10 GSM806934_UCSF-UBC.Fetal_Brain.H3K4me1.HuFNSC02.sga Fetal Brain|H3K4me1|rep 2 H3K4me1 GSM806934
11 GSM806942_UCSF-UBC.Fetal_Brain.H3K4me1.HuFNSC01.sga Fetal Brain|H3K4me1|rep 3 H3K4me1 GSM806942
12 GSM621457_BI.Fetal_Brain.H3K4me3.UW_H-22510.sga Fetal Brain|H3K4me3|rep 1 H3K4me3 GSM621457
13 GSM669624_UCSF-UBC.Fetal_Brain.H3K4me3.HuFNSC-T.sga Fetal Brain|H3K4me3|rep 2 H3K4me3 GSM669624
14 GSM806935_UCSF-UBC.Fetal_Brain.H3K4me3.HuFNSC02.sga Fetal Brain|H3K4me3|rep 3 H3K4me3 GSM806935
15 GSM806943_UCSF-UBC.Fetal_Brain.H3K4me3.HuFNSC01.sga Fetal Brain|H3K4me3|rep 4 H3K4me3 GSM806943
16 GSM669623_UCSF-UBC.Fetal_Brain.H3K9ac.HuFNSC-T.sga Fetal Brain|H3K9ac H3K9ac GSM669623
17 GSM621427_BI.Fetal_Brain.H3K9me3.UW_H-22510.sga Fetal Brain|H3K9me3|rep 1 H3K9me3 GSM621427
18 GSM806936_UCSF-UBC.Fetal_Brain.H3K9me3.HuFNSC02.sga Fetal Brain|H3K9me3|rep 2 H3K9me3 GSM806936
19 GSM806944_UCSF-UBC.Fetal_Brain.H3K9me3.HuFNSC01.sga Fetal Brain|H3K9me3|rep 3 H3K9me3 GSM806944
20 GSM916054_BI.Fetal_Brain.H3K9me3.UW_H22676.sga Fetal Brain|H3K9me3|rep 4 H3K9me3 GSM916054
21 GSM806948_UCSF-UBC.Fetal_Brain.Input.HuFNSC01.sga Fetal Brain|Input|rep 1 Input GSM806948
22 GSM817243_UCSF-UBC.Fetal_Brain.Input.HuFNSC02.sga Fetal Brain|Input|rep 2 Input GSM817243
23 GSM669944_BI.Fetal_Brain.Input.UW_H23284.sga Fetal Brain|Input|rep 3 WCE GSM669944
24 GSM706851_BI.Fetal_Brain.Input.UW_H22676.sga Fetal Brain|Input|rep 4 WCE GSM706851

DNase FAIRE data:

Filename Description Feature GEO-ID
1 GSM723021_UW.Fetal_Brain.Digital_Genomic_Footprinting.H-22510.DGF.DS11872.sga Fetal Brain|DNase-HS DNase-HS GSM723021
2 GSM1027328_UW.Fetal_Brain.ChromatinAccessibility.H-24510.DNase.DS20780.sga Fetal Brain|DNase-seq|rep 1 DNase-seq GSM1027328
3 GSM665819_UW.Fetal_Brain.ChromatinAccessibility.H-23548.DS16302.sga Fetal Brain|DNase-seq|rep 10 DNase-seq GSM665819
4 GSM878650_UW.Fetal_Brain.ChromatinAccessibility.H-24279.DS20221.sga Fetal Brain|DNase-seq|rep 11 DNase-seq GSM878650
5 GSM878651_UW.Fetal_Brain.ChromatinAccessibility.H-24297.DS20226.sga Fetal Brain|DNase-seq|rep 12 DNase-seq GSM878651
6 GSM878652_UW.Fetal_Brain.ChromatinAccessibility.H-24381.DS20231.sga Fetal Brain|DNase-seq|rep 13 DNase-seq GSM878652
7 GSM530651_UW.Fetal_Brain.ChromatinAccessibility.H-22510.DS11872.sga Fetal Brain|DNase-seq|rep 2 DNase-seq GSM530651
8 GSM595913_UW.Fetal_Brain.ChromatinAccessibility.H-22510.DS11877.sga Fetal Brain|DNase-seq|rep 3 DNase-seq GSM595913
9 GSM595920_UW.Fetal_Brain.ChromatinAccessibility.H-22911.DS14464.sga Fetal Brain|DNase-seq|rep 4 DNase-seq GSM595920
10 GSM595922_UW.Fetal_Brain.ChromatinAccessibility.H-23266.DS14717.sga Fetal Brain|DNase-seq|rep 5 DNase-seq GSM595922
11 GSM595923_UW.Fetal_Brain.ChromatinAccessibility.H-23266.DS14718.sga Fetal Brain|DNase-seq|rep 6 DNase-seq GSM595923
12 GSM595926_UW.Fetal_Brain.ChromatinAccessibility.H-23284.DS14803.sga Fetal Brain|DNase-seq|rep 7 DNase-seq GSM595926
13 GSM595928_UW.Fetal_Brain.ChromatinAccessibility.H-23284.DS14815.sga Fetal Brain|DNase-seq|rep 8 DNase-seq GSM595928
14 GSM665804_UW.Fetal_Brain.ChromatinAccessibility.H-23399.DS15453.sga Fetal Brain|DNase-seq|rep 9 DNase-seq GSM665804
15 GSM1027308_UW.Fetal_Spinal_Cord.ChromatinAccessibility.H-24244.DNase.DS19260.sga Fetal Spinal Cord|DNase-seq|rep 1 DNase-seq GSM1027308
16 GSM1027339_UW.Fetal_Spinal_Cord.ChromatinAccessibility.H-24582.DNase.DS20956.sga Fetal Spinal Cord|DNase-seq|rep 2 DNase-seq GSM1027339
17 GSM817189_UW.Fetal_Spinal_Cord.ChromatinAccessibility.H-24111.DS18501.sga Fetal Spinal Cord|DNase-seq|rep 3 DNase-seq GSM817189
18 GSM878661_UW.Fetal_Spinal_Cord.ChromatinAccessibility.H-24409.DS20351.sga Fetal Spinal Cord|DNase-seq|rep 4 DNase-seq GSM878661
19 GSM878663_UW.Fetal_Spinal_Cord.ChromatinAccessibility.H-24493.DS20530.sga Fetal Spinal Cord|DNase-seq|rep 5 DNase-seq GSM878663

Technical Notes

BED files were downloaded from the GEO FTP server and converted in SGA format using using bed2sga.pl (ChIP-Seq v. 1.5.2).

References

Last update: 8 Feb 2016