Teves 2011, Genome wide nucleosome and Pol-II maps in S2 cells after HS treatment. LiftOver from dm3.

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: GSE30755
• Input file format: SRA
• Download date: n/a

From D. melanogaster (Aug 2014 BDGP Rel6 + ISO1 MT/dm6).

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

Dataset lifted over from dm3

• 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