Chodavarapu 2010, Nucleosome positioning in shoots.

Nucleosome maps (MNase-seq samples) and histon H3 map in A. thaliana shoots grown under continuous light for three weeks.

• Raw data was downloaded from: GEO
• Input file format: SRA
• Download date: 25-11-2016

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

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM543297.sga	Shoot|H3	H3	GSM543297

DNase FAIRE data:

	Filename	Description	Feature	GEO-ID
1	GSM543295.sga	Shoot|Nucleosomes|rep1	Mnase-Seq	GSM543295
2	GSM543296.sga	Shoot|Nucleosomes|rep2	Mnase-Seq	GSM543296

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).

• Chodavarapu RK, Feng S, Bernatavichute YV, Chen PY, Stroud H, Yu Y, Hetzel JA, Kuo F, Kim J, Cokus SJ, Casero D, Bernal M, Huijser P, Clark AT, Krämer U, Merchant SS, Zhang X, Jacobsen SE, Pellegrini M
  Relationship between nucleosome positioning and DNA methylation. Nature. 2010 Jul 15;466(7304):388-92. doi: 10.1038/nature09147. Epub 2010 May 30. 20512117
• GEO series GSE21821: Relationship between nucleosome positioning and DNA methylation: Bisulfite-Seq, ChIP-Seq, and Mnase-Seq

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