Chromatin maps and histone marks in developing ears.

Description

Chromatin map and histon marks in Z. mays variety B73 during ear develpment.

Source

Samples

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

DNase FAIRE data:

Filename Description Feature GEO-ID
1 B73_developing_ear_chromatin_1-min.sga B73 developing ear|chromatin|1-min chromatin -
2 B73_developing_ear_chromatin_16-min.sga B73 developing ear|chromatin|16-min chromatin -
3 B73_developing_ear_chromatin_4-min.sga B73 developing ear|chromatin|4-min chromatin -

ChIP-seq data:

Filename Description Feature GEO-ID
1 B73_developing_ears_H3K27me2_rep1.sga B73 developing ears|H3K27me2|rep1 H3K27me2 -
2 B73_developing_ears_H3K27me2_rep2.sga B73 developing ears|H3K27me2|rep2 H3K27me2 -
3 B73_developing_ears_H3K9me2_rep1.sga B73 developing ears|H3K9me2|rep1 H3K9me2 -
4 B73_developing_ears_H3K9me2_rep2.sga B73 developing ears|H3K9me2|rep2 H3K9me2 -

Technical Notes

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the genome using Bowtie2 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).

Last update: 14 Dec 2016