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.



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

Technical Notes

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 (ChIP-Seq v. 1.5.3).


Last update: 1 Oct 2018