Liu 2015, Leaves chromatin maps treated with Coronatine.

Description

Nucleosome maps of rosette leaves treated and untreated with coronatine (samples named COR and Control respectively). An additional control (naked DNA) is also present.

Source

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

Samples

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

DNase FAIRE data:

	Filename	Description	Feature	GEO-ID
1	GSM1570248.sga	Leaves\|Nucleosome-gDNA\|control\|rep1;	MNase	GSM1570248
2	GSM1570249.sga	Leaves\|Nucleosome-gDNA\|control\|rep2;	MNase	GSM1570249
3	GSM1570250.sga	Leaves\|Nucleosome-gDNA\|COR\|rep1;	MNase	GSM1570250
4	GSM1570251.sga	Leaves\|Nucleosome-gDNA\|COR\|rep2;	MNase	GSM1570251
5	GSM1570252.sga	Leaves\|Naked-gDNA\|control\|rep1;	MNase	GSM1570252

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

Liu MJ, Seddon AE, Tsai ZT, Major IT, Floer M, Howe GA, Shiu SH
Determinants of nucleosome positioning and their influence on plant gene expression. Genome Res. 2015 Aug;25(8):1182-95. doi: 10.1101/gr.188680.114. Epub 2015 Jun 10. 26063739
GEO series GSE64397: Determinants of nucleosome positioning and their influence on plant gene expression

Last update: 8 Oct 2018