Li 2014, Chromatin maps of WT and mutant seedlings.

Description

Chromatin maps of wild type A. thaliana seedlings (Col-0) and a double mutant in the AtISWI genes CHROMATIN REMODELING 11 (CHR11) and CHR17, two chromatin remodelers.

Source

Raw data was downloaded from: GEO
Input file format: SRA
Download date: 09-12-2016

Samples

From A. thaliana (Feb 2011 TAIR10/araTha1).

DNase FAIRE data:

	Filename	Description	Feature	GEO-ID
1	GSM1216734.sga	Seedling\|chr11-1 chr17-1	MNase	GSM1216734
2	GSM1216733.sga	Seedlings\|Col-0	MNase	GSM1216733

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

Li G, Liu S, Wang J, He J, Huang H, Zhang Y, Xu L
ISWI proteins participate in the genome-wide nucleosome distribution in Arabidopsis. Plant J. 2014 May;78(4):706-14. doi: 10.1111/tpj.12499. Epub 2014 Apr 15. 24606212
GEO series GSE50242: MNase-seq analysis of Col-0 and chr11-1 chr17-1

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Last update: 1 Oct 2018