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.



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

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 (ChIP-Seq v. 1.5.2).


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Last update: 1 Oct 2018