Ziller 2015, Epigenetic footprints during neural differentiation.

Histone modification maps (H3K27ac, H3K27me3, H3K4me1, H3K4me3) in human ES cells undergoing neural differentiation.

• Raw data was downloaded from SRA: =SRP048761
• Input file format: SRA
• Download date: 29-03-2016

From H. sapiens (Feb 2009 GRCh37/hg19).

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM1521740.sga	ERG|H3K27ac|rep1	H3K27ac	GSM1521740
2	GSM1521745.sga	ERG|H3K27ac|rep2	H3K27ac	GSM1521745
3	GSM1521741.sga	ERG|H3K27me3|rep1	H3K27me3	GSM1521741
4	GSM1521746.sga	ERG|H3K27me3|rep2	H3K27me3	GSM1521746
5	GSM1521742.sga	ERG|H3K4me1|rep1	H3K4me1	GSM1521742
6	GSM1521747.sga	ERG|H3K4me1|rep2	H3K4me1	GSM1521747
7	GSM1521743.sga	ERG|H3K4me3|rep1	H3K4me3	GSM1521743
8	GSM1521748.sga	ERG|H3K4me3|rep2	H3K4me3	GSM1521748
9	GSM1521744.sga	ERG|WCE|rep1	WCE	GSM1521744
10	GSM1521749.sga	ERG|WCE|rep2	WCE	GSM1521749
11	GSM1521721.sga	ESC|H3K27ac|rep1	H3K27ac	GSM1521721
12	GSM1521726.sga	ESC|H3K27ac|rep2	H3K27ac	GSM1521726
13	GSM1521722.sga	ESC|H3K27me3|rep1	H3K27me3	GSM1521722
14	GSM1521727.sga	ESC|H3K27me3|rep2	H3K27me3	GSM1521727
15	GSM1521723.sga	ESC|H3K4me1|rep1	H3K4me1	GSM1521723
16	GSM1521728.sga	ESC|H3K4me1|rep2	H3K4me1	GSM1521728
17	GSM1521724.sga	ESC|H3K4me3|rep1	H3K4me3	GSM1521724
18	GSM1521729.sga	ESC|H3K4me3|rep2	H3K4me3	GSM1521729
19	GSM1521725.sga	ESC|WCE|rep1	WCE	GSM1521725
20	GSM1521750.sga	MRG|H3K27ac|rep1	H3K27ac	GSM1521750
21	GSM1521755.sga	MRG|H3K27ac|rep2	H3K27ac	GSM1521755
22	GSM1521751.sga	MRG|H3K27me3|rep1	H3K27me3	GSM1521751
23	GSM1521756.sga	MRG|H3K27me3|rep2	H3K27me3	GSM1521756
24	GSM1521752.sga	MRG|H3K4me1|rep1	H3K4me1	GSM1521752
25	GSM1521757.sga	MRG|H3K4me1|rep2	H3K4me1	GSM1521757
26	GSM1521753.sga	MRG|H3K4me3|rep1	H3K4me3	GSM1521753
27	GSM1521758.sga	MRG|H3K4me3|rep2	H3K4me3	GSM1521758
28	GSM1521761.sga	MRG|OTX2|rep1	OTX2	GSM1521761
29	GSM1521754.sga	MRG|WCE|rep1	WCE	GSM1521754
30	GSM1521759.sga	MRG|WCE|rep2	WCE	GSM1521759
31	GSM1521730.sga	NE|H3K27ac|rep1	H3K27ac	GSM1521730
32	GSM1521735.sga	NE|H3K27ac|rep2	H3K27ac	GSM1521735
33	GSM1521731.sga	NE|H3K27me3|rep1	H3K27me3	GSM1521731
34	GSM1521736.sga	NE|H3K27me3|rep2	H3K27me3	GSM1521736
35	GSM1521732.sga	NE|H3K4me1|rep1	H3K4me1	GSM1521732
36	GSM1521737.sga	NE|H3K4me1|rep2	H3K4me1	GSM1521737
37	GSM1521733.sga	NE|H3K4me3|rep1	H3K4me3	GSM1521733
38	GSM1521738.sga	NE|H3K4me3|rep2	H3K4me3	GSM1521738
39	GSM1521760.sga	NE|OTX2|rep1	OTX2	GSM1521760
40	GSM1521734.sga	NE|WCE|rep1	WCE	GSM1521734
41	GSM1521739.sga	NE|WCE|rep2	WCE	GSM1521739

Notes on samples nomenclature:

Cell types:

• ERG: early radial glial
• ESC: embryonic stem cells
• MRG: mid radial glial
• NE: neuroepithelial

Sample types:

• WCE: control samples

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the genome using Bowtie v0.12.8. SAM files were then converted into bam using samtools v0.1.14 and to bed using bamToBed v2.12.0 (bedtools). SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.2).

• Ziller MJ, Edri R, Yaffe Y, Donaghey J, Pop R, Mallard W, Issner R, Gifford CA, Goren A, Xing J, Gu H, Cacchiarelli D, Tsankov AM, Epstein C, Rinn JL, Mikkelsen TS, Kohlbacher O, Gnirke A, Bernstein BE, Elkabetz Y, Meissner A
  Dissecting neural differentiation regulatory networks through epigenetic footprinting. Nature. 2015 Feb 19;518(7539):355-9. doi: 10.1038/nature13990. Epub 2014 Dec 24. 25533951
• GEO series GSE62193: Dissecting neural differentiation regulatory networks through epigenetic footprinting