Bonn 2012, Analisys of H3 modifications in mesoderm.

ChIP-seq against several histone modifications, PolII and Mef2 in mesodermal cells of D. malanogaster.

• Raw data was downloaded from ENA : PRJEB2454
• Input file format: BAM

From D. melanogaster (Apr 2006 BDGP R5/dm3).

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	ERR031126.sga	Mesoderm|input||rep1	input	-
2	ERR031127.sga	Mesoderm|input||rep2	input	-
3	ERR031128.sga	Mesoderm|H3||rep1	H3	-
4	ERR031129.sga	Mesoderm|H3||rep2	H3	-
5	ERR031130.sga	Mesoderm|H3K27ac||rep1	H3K27ac	-
6	ERR031131.sga	Mesoderm|H3K27ac||rep2	H3K27ac	-
7	ERR031132.sga	Mesoderm|H3K4me1||rep1	H3K4me1	-
8	ERR031133.sga	Mesoderm|H3K4me1||rep2	H3K4me1	-
9	ERR031134.sga	Mesoderm|H3K4me3||rep1	H3K4me3	-
10	ERR031135.sga	Mesoderm|H3K4me3||rep2	H3K4me3	-
11	ERR031136.sga	Mesoderm|H3K36me3||rep1	H3K36me3	-
12	ERR031137.sga	Mesoderm|H3K36me3||rep2	H3K36me3	-
13	ERR031138.sga	Mesoderm|H3K79me3||rep1	H3K79me3	-
14	ERR031139.sga	Mesoderm|H3K79me3||rep2	H3K79me3	-
15	ERR031140.sga	Mesoderm|H3K27me3||rep1	H3K27me3	-
16	ERR031141.sga	Mesoderm|H3K27me3||rep2	H3K27me3	-
17	ERR031142.sga	Mesoderm|PolII||rep1	PolII	-
18	ERR031143.sga	Mesoderm|PolII||rep2	PolII	-
19	ERR031144.sga	Mesoderm|BiTS_Mef2	Mef2	-
20	ERR031145.sga	Mesoderm|Mef2||rep1	Mef2	-
21	ERR031146.sga	Mesoderm|Mef2||rep2	Mef2	-

Notes on samples nomenclature:

BiTS_Mef2 : Batch isolation of tissue-specific chromatin for immunoprecipitation targeted at Mef2.

BAM files were downloaded from EBI and converted to bed using bamToBed v2.12.0 (bedtools). SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.3).

• Bonn S, Zinzen RP, Girardot C, Gustafson EH, Perez-Gonzalez A, Delhomme N, Ghavi-Helm Y, Wilczyński B, Riddell A, Furlong EE
  Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development. Nat Genet. 2012 Jan 8;44(2):148-56. doi: 10.1038/ng.1064. 22231485