Maatouk 2017, Genome-wide identification of regulatory elements in Sertoli cells.

Genome-wide identification of regulatory elements in preSertoli cells based on DNaseI hypersensitivity. One biological replicate was analyzed for each of the eight mouse samples using DNase-seq. Two biological replicates for ChIP-seq (H3K27ac).

• Raw data was downloaded from: SRA
• Input file format: SRA
• Download date: 22-3-2018

From M. musculus (July 2007 NCBI37/mm9).

DNase FAIRE data:

	Filename	Description	Feature	GEO-ID
1	GSM1281689	ES|cell culture	DNase	GSM1281689
2	GSM1281690	Primary fibroblast|cell culture	DNase	GSM1281690
3	GSM1856274	Testis|E13.5 embryos	DNase	GSM1856274
4	GSM1281688	Testis|E15.5 embryos	DNase	GSM1281688
5	GSM1281691	Whole brain|adult	DNase	GSM1281691
6	GSM1281692	Whole heart|adult	DNase	GSM1281692
7	GSM1281693	Whole kidney|adult	DNase	GSM1281693
8	GSM1281694	Whole liver|adult	DNase	GSM1281694

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM1864823	Testis|E13.5|H3K27ac|rep1	H3K27ac	GSM1864823
2	GSM1864824	Testis|E13.5|H3K27ac|rep2	H3K27ac	GSM1864824
3	GSM1864825	Testis|E13.5|input|rep1	input	GSM1864825
4	GSM1864826	Testis|E13.5|input|rep2	input	GSM1864826

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. As explained in the manuscript, only the first 20bp of each read were used for mapping, the others been adapters. 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).

• Maatouk DM, Natarajan A, Shibata Y, Song L, Crawford GE, Ohler U, Capel B
  Genome-wide identification of regulatory elements in Sertoli cells. Development. 2017 Feb 15;144(4):720-730. doi: 10.1242/dev.142554. Epub 2017 Jan 13. 28087634
• GEO series GSE53076: Genome-wide identification of regulatory elements in preSertoli cells based on DNaseI hypersensitivity