Genome-wide mapping of various histone modifications.

Genome-wide mapping of H3K27me3, H3K36me3, H3K4me3 and H3K9ac in shoot and root tissues for the B73 cultivar.

• Raw data was downloaded from: GEO
• Input file format: SRA
• Download date: 14-06-2016

From Z. mays (Oct 2013 B73 RefGen_v3/zm3).

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM381721.sga	root|H3K27me3|rep	H3K27me3	GSM381721
2	GSM381723.sga	root|H3K36me3|rep	H3K36me3	GSM381723
3	GSM381717.sga	root|H3K4me3|rep	H3K4me3	GSM381717
4	GSM381719.sga	root|H3K9ac|rep	H3K9ac	GSM381719
5	GSM381699.sga	shoot|H3K27me3|rep	H3K27me3	GSM381699
6	GSM381701.sga	shoot|H3K36me3|rep	H3K36me3	GSM381701
7	GSM381695.sga	shoot|H3K4me3|rep	H3K4me3	GSM381695
8	GSM381697.sga	shoot|H3K9ac|rep	H3K9ac	GSM381697

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).

• Wang X, Elling AA, Li X, Li N, Peng Z, He G, Sun H, Qi Y, Liu XS, Deng XW
  Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell. 2009 Apr;21(4):1053-69. doi: 10.1105/tpc.109.065714. Epub 2009 Apr 17. 19376930