Ercan 2011, Nucleosome occupancy profiling by high throughput sequencing.

Nucleosome occupancy profiles of different developmental stages in C. elegans: embryos, germlineless adults, germ line containing adults, and XO hermaphrodites at L3 larval stage. A control sample is also present.

• Raw data was downloaded from: GEO
• Input file format: SRA
• Download date: n/a

From C. elegans (May 2008 WS190/ce6).

DNase FAIRE data:

	Filename	Description	Feature	GEO-ID
1	GSM514735.sga	Mixed stage embryos	MNase	GSM514735
2	GSM514736.sga	Young germline-less adults	MNase	GSM514736
3	GSM590213.sga	Young germline containing adults	MNase	GSM590213
4	GSM590214.sga	L3 stage XO hermaphrodites	MNase	GSM590214
5	GSM590215.sga	Control sample	MNase	GSM590215

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. 1.5.3).

• Ercan S, Lubling Y, Segal E, Lieb JD
  High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans. Genome Res. 2011 Feb;21(2):237-44. doi: 10.1101/gr.115931.110. Epub 2010 Dec 22. 21177966
• GEO series GSE20136: Genome-wide nucleosome occupancy profiling by high throughput sequencing, and microarray analysis of RNA abundance