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

Description

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

Source

Samples

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

Technical Notes

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).

References

Last update: 1 Oct 2018