Teves 2011, Genome wide nucleosome and Pol-II maps in S2 cells after HS treatment.

Intact nuclei of D. melanogaster S2 cells were extracted and processed to isolate "active" chromatin (low salt concentration: 80mM), "inactive" chromatin (high salt concentration: 350mM) and total chromatin.

Several treatments were aplied to the cells:

• Control: no treatment
• HS: heat shock, 37 C for 15 min
• DRB: 5,6-dichlorobenzimidazole for 10 min to induce Pol II stalling
• DRB-HS: DRB for 10 min followed by HS for 15 min

Several techniques were used:

• ChIP-seq of Pol-II enzyme
• Chromatine MNase-seq of monomucleosomes
• CATCH-IT, Covalent Attachment of Tagged Histones to Capture and Identify Turnover

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

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

DNase FAIRE data:

	Filename	Description	Feature	GEO-ID
1	GSM763041.sga	S2|Nuclesosome|Total|control	Nucleosome	GSM763041
2	GSM1293957.sga	S2|Nuclesosome|Total|HS	Nucleosome	GSM1293957
3	GSM1293955.sga	S2|Nuclesosome|Total|DRB	Nucleosome	GSM1293955
4	GSM1293956.sga	S2|Nuclesosome|Total|DRB-HS	Nucleosome	GSM1293956
5	GSM763027.sga	S2|Nuclesosome|350mM salt|control	Nucleosome	GSM763027
6	GSM763028.sga	S2|Nuclesosome|350mM salt|HS	Nucleosome	GSM763028
7	GSM763029.sga	S2|Nuclesosome|350mM salt|DRB	Nucleosome	GSM763029
8	GSM763030.sga	S2|Nuclesosome|80mM salt|control	Nucleosome	GSM763030
9	GSM763031.sga	S2|Nuclesosome|80mM salt|HS	Nucleosome	GSM763031
10	GSM763032.sga	S2|Nuclesosome|80mM salt|DRB	Nucleosome	GSM763032
11	GSM763033.sga	S2|Nuclesosome|80mM salt|DRB-HS	Nucleosome	GSM763033
12	GSM763034.sga	S2|Nuclesosome|CATCH-IT|control	Nucleosome	GSM763034
13	GSM763035.sga	S2|Nuclesosome|CATCH-IT|HS	Nucleosome	GSM763035
14	GSM763036.sga	S2|Nuclesosome|CATCH-IT|DRB	Nucleosome	GSM763036

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM763037.sga	S2|PolII|80mMsalt|control	PolII	GSM763037
2	GSM763038.sga	S2|PolII|80mMsalt|HS	PolII	GSM763038
3	GSM763039.sga	S2|PolII|80mMsalt|DRB	PolII	GSM763039
4	GSM763040.sga	S2|PolII|80mMsalt|DRB-HS	PolII	GSM763040

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 paired-end reads. 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).

• Teves SS, Henikoff S
  Heat shock reduces stalled RNA polymerase II and nucleosome turnover genome-wide. Genes Dev. 2011 Nov 15;25(22):2387-97. doi: 10.1101/gad.178079.111. 22085965
• GEO series GSE30755: Genome-wide reductions in active chromatin, paused RNA Polymerase II and nucleosome turnover during heat shock