Bohla 2014, CTCF/CP190 and ISWI dependent regulation of nucleosome occupancy.

Changes in chromatin organisation are investigated for two RNAi lines: CTCS (an insulator) and ISWI (a component of the nucleosome remodelling factor NURF). Moreover a luciferase control is also investigated.

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

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

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM1248973.sga	H3|ISWI RNAi	H3	GSM1248973
2	GSM1248972.sga	H3|CTCF CP190 RNAi	H3	GSM1248972
3	GSM1248971.sga	H3|luciferase RNAi	H3	GSM1248971

DNase FAIRE data:

	Filename	Description	Feature	GEO-ID
1	GSM1248976.sga	MNase|ISWI RNAi	MNase	GSM1248976
2	GSM1248975.sga	MNase|CTCF CP190 RNAi	MNase	GSM1248975
3	GSM1248974.sga	MNase|luciferase RNAi	MNase	GSM1248974

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).

• Bohla D, Herold M, Panzer I, Buxa MK, Ali T, Demmers J, Krüger M, Scharfe M, Jarek M, Bartkuhn M, Renkawitz R
  A functional insulator screen identifies NURF and dREAM components to be required for enhancer-blocking. PLoS One. 2014 Sep 23;9(9):e107765. doi: 10.1371/journal.pone.0107765. eCollection 2014. 25247414
• GEO series GSE51600: CTCF/CP190 and ISWI dependent regulation of nucleosome occupancy