Gent 2014, Chromatin maps and histone marks in developing ears.

Chromatin maps and histone marks in Z. mays variety B73 during ear development.

• Raw data was downloaded from: NCBI
• Input file format: SRA
• Download date: 14-12-2016

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	-

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).

Gent J, Madzima TF, Bader R, Kent MR, Zhang X1, Stam M, McGinnis KM, Dawe RK
Accessible DNA and relative depletion of H3K9me2 at maize loci undergoing RNA-directed DNA methylation. Plant Cell. 2014 Dec;26(12):4903-17. doi: 10.1105/tpc.114.130427. Epub 2014 Dec 2. 25465407

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