Davie 2015, ATAC and FAIRE-seq for the discovery of regulatory regions driving tumor development.

FAIRE-Seq in Drosophila wild type eye-antennal imaginal discs (Control samples, 2 wt strains: WT and CantonS); ATAC-Seq in Drosophila wild type eye-antennal imaginal discs (Control samples, 3 wt strains: WT, RAL-208, Optix-GFP) ; FAIRE-Seq in Drosophila Ras/Scrib induced eye disc tumors (1 early and 1 late); ATAC-Seq in Drosophila Ras/Scrib induced eye disc tumors (1 early and 1 late); ATAC-Seq in Drosophila eye discs with Unpaired (UPD) over-expression (2 biological replicates); CTCF ChIP-seq in Drosophila eye discs; ChIP-seq input in Drosophila eye discs

• Raw data was downloaded from: SRA
• Input file format: SRA
• Download date: 29-3-2018

From D. melanogaster (Apr 2006 BDGP R5/dm3).

DNase FAIRE data:

	Filename	Description	Feature	GEO-ID
1	GSM1426254.sga	WT|ATAC|Control	ATAC	GSM1426254
2	GSM1426255.sga	RAL-208|ATAC|Control	ATAC	GSM1426255
3	GSM1426256.sga	Optix-GFP|ATAC|Control	ATAC	GSM1426256
4	GSM1426257.sga	RasScrib-Early|ATAC	ATAC	GSM1426257
5	GSM1426258.sga	RasScrib-Late|ATAC	ATAC	GSM1426258
6	GSM1426259.sga	UPD-Overexpression|ATAC|Rep1	ATAC	GSM1426259
7	GSM1426260.sga	UPD-Overexpression|ATAC|Rep2	ATAC	GSM1426260
8	GSM1426261.sga	WT|FAIRE|Control	FAIRE	GSM1426261
9	GSM1426262.sga	CantonS|FAIRE|Control	FAIRE	GSM1426262
10	GSM1426263.sga	RasScrib-Early|FAIRE	FAIRE	GSM1426263
11	GSM1426264.sga	RasScrib-Late|FAIRE	FAIRE	GSM1426264

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM1426265.sga	CantonS|CTCF	CTCF	GSM1426265
2	GSM1426266.sga	CantonS|input	input	GSM1426266

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the genome using Bowtie2 v2.25. 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).

• Davie K, Jacobs J, Atkins M, Potier D, Christiaens V, Halder G, Aerts S
  Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling. PLoS Genet. 2015 Feb 13;11(2):e1004994. doi: 10.1371/journal.pgen.1004994. eCollection 2015 Feb. 25679813
• GEO series GSE59078: Discovery of Transcription Factors and Regulatory Regions Driving In Vivo Tumor Development by ATAC-seq and FAIRE-seq Open Chromatin Profiling