Tiwari 2011, Histone modifications and TFs on three stem cell lines.

ChIP-seq against H3K27me3, H3K4me2, RNA Pol II, JNK(c-Jun NH2-terminal kinase) 1 or 3 and NF-YA(Nuclear transcription factor Y subunit alpha) in embryonic stem (ES), neural progenitor (NP) and terminally differentiated pyramidal glutamatergic neurons (TN) cells.

• Raw data was downloaded from: GEO
• Input file format: SRA
• Download date: 10-06-2012

From M. musculus (July 2007 NCBI37/mm9).

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	ES_H3K27me3.sga	ES H3K27me3	H3K27me3	-
2	ES_H3K4me2.sga	ES H3K4me2	H3K4me2	-
3	ES_JNK13.sga	ES JNK13	JNK13	-
4	ES_NFYA.sga	ES NFYA	NFYA	-
5	ES_PolII.sga	ES PolII	PolII	-
6	NP_H3K27me3.sga	NP H3K27me3	H3K27me3	-
7	NP_H3K4me2.sga	NP H3K4me2	H3K4me2	-
8	NP_JNK13.sga	NP JNK13	JNK13	-
9	NP_NFYA.sga	NP NFYA	NFYA	-
10	NP_PolII.sga	NP PolII	PolII	-
11	TN_DMSO.sga	TN DMSO	DMSO	-
12	TN_H3K27me3.sga	TN H3K27me3	H3K27me3	-
13	TN_H3K4me2.sga	TN H3K4me2	H3K4me2	-
14	TN_JNK13.sga	TN JNK13	JNK13	-
15	TN_NFYA.sga	TN NFYA	NFYA	-
16	TN_PolII.sga	TN PolII	PolII	-
17	GSM632032-ES_H3K27me3_TechRep-a1.sga	ES H3K27me3 TechRep-a1	H3K27me3	GSM632032
18	GSM632033-ES_H3K27me3_TechRep.sga	ES H3K27me3 TechRep-a2	H3K27me3	GSM632033
19	GSM632034-ES_H3K27me3_BioRep-b1.sga	ES H3K27me3 BioRep-b1	H3K27me3	GSM632034
20	GSM632035-ES_H3K4me2.sga	ES H3K4me2	H3K4me2	GSM632035
21	GSM632036-ES_JNK13_BioRep-a.sga	ES JNK13 BioRep-a	JNK13	GSM632036
22	GSM632037-ES_JNK13_BioRep-b.sga	ES JNK13 BioRep-b	JNK13	GSM632037
23	GSM632038-ES_NFYA_BioRep-a.sga	ES NFYA BioRep-a	NFYA	GSM632038
24	GSM632039-ES_NFYA_BioRep-b.sga	ES NFYA BioRep-b	NFYA	GSM632039
25	GSM632040-ES_PolII.sga	ES PolII	PolII	GSM632040
26	GSM632041-Input.sga	ES Input	Input	GSM632041
27	GSM632042-NP_H3K27me3_TechRep-a1.sga	NP H3K27me3 TechRep-a1	H3K27me3	GSM632042
28	GSM632043-NP_H3K27me3_TechRep.sga	NP H3K27me3 TechRep-a2	H3K27me3	GSM632043
29	GSM632044-NP_H3K27me3_BioRep-b1.sga	NP H3K27me3 BioRep-b1	H3K27me3	GSM632044
30	GSM632045-NP_H3K4me2.sga	NP H3K4me2	H3K4me2	GSM632045
31	GSM632046-NP_JNK13_BioRep-a.sga	NP JNK13 BioRep-a	JNK13	GSM632046
32	GSM632047-NP_JNK13_BioRep-b.sga	NP JNK13 BioRep-b	JNK13	GSM632047
33	GSM632048-NP_NFYA_BioRep-a.sga	NP NFYA BioRep-a	NFYA	GSM632048
34	GSM632049-NP_NFYA_BioRep-b.sga	NP NFYA BioRep-b	NFYA	GSM632049
35	GSM632050-NP_PolII.sga	NP PolII	PolII	GSM632050
36	GSM632051-TN_H3K27me3_TechRep-a1.sga	TN H3K27me3 TechRep-a1	H3K27me3	GSM632051
37	GSM632052-TN_H3K27me3_TechRep.sga	TN H3K27me3 TechRep-a2	H3K27me3	GSM632052
38	GSM632053-TN_H3K27me3_BioRep-b1.sga	TN H3K27me3 BioRep-b1	H3K27me3	GSM632053
39	GSM632054-TN_H3K4me2.sga	TN H3K4me2	H3K4me2	GSM632054
40	GSM632055-TN_JNK13_BioRep-a.sga	TN JNK13 BioRep-a	JNK13	GSM632055
41	GSM632056-TN_JNK13_BioRep-b.sga	TN JNK13 BioRep-b	JNK13	GSM632056
42	GSM632057-TN_NFYA_BioRep-a.sga	TN NFYA BioRep-a	NFYA	GSM632057
43	GSM632058-TN_NFYA_BioRep-b.sga	TN NFYA BioRep-b	NFYA	GSM632058
44	GSM632059-TN_PolII.sga	TN PolII	PolII	GSM632059
45	GSM768537-TN_DMSO_JNK13.sga	TN JNK13 DMSO	JNK13	GSM768537

Merged samples:

When present, technical and biological replicates were merged together to generate a new sample. For example sample 'ES H3K27me3' is the result of merging 3 replicates: 'ES H3K27me3 TechRep-a1', 'ES H3K27me3 TechRep-a2' and 'ES H3K27me3 BioRep-b1'.

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).

• Tiwari VK, Stadler MB, Wirbelauer C, Paro R, Schübeler D, Beisel C
  A chromatin-modifying function of JNK during stem cell differentiation. Nat Genet. 2011 Dec 18;44(1):94-100. doi: 10.1038/ng.1036. 22179133
• GEO series GSE25532: A chromatin-modifying function of JNK during stem cell differentiation