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

Description

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.

Source

Samples

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'.

Technical Notes

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).

References

Last update: 10 Mar 2017