Teves 11, Genome wide nucleosome and Pol-II maps in S2 cells after HS treatment.

Description

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:

Several techniques were used:

Source

Raw data can be downloaded from: GEO dataset GSE30755

Samples

From D. melanogaster genome dm3.

Filename Description Feature GEO-ID
1 GSM763041.sga S2|Nuclesosome|Total|control Nucleosome -
2 GSM1293957.sga S2|Nuclesosome|Total|HS Nucleosome -
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 -
7 GSM763029.sga S2|Nuclesosome|350mM salt|DRB Nucleosome -
8 GSM763030.sga S2|Nuclesosome|80mM salt|control Nucleosome -
9 GSM763031.sga S2|Nuclesosome|80mM salt|HS Nucleosome -
10 GSM763032.sga S2|Nuclesosome|80mM salt|DRB Nucleosome -
11 GSM763033.sga S2|Nuclesosome|80mM salt|DRB-HS Nucleosome -
12 GSM763034.sga S2|Nuclesosome|CATCH-IT|control Nucleosome -
13 GSM763035.sga S2|Nuclesosome|CATCH-IT|HS Nucleosome -
14 GSM763036.sga S2|Nuclesosome|CATCH-IT|DRB Nucleosome -
15 GSM763037.sga S2|PolII|80mMsalt|control PolII GSM763037
16 GSM763038.sga S2|PolII|80mMsalt|HS PolII GSM763038
17 GSM763039.sga S2|PolII|80mMsalt|DRB PolII GSM763039
18 GSM763040.sga S2|PolII|80mMsalt|DRB-HS PolII GSM763040

Technical Notes

Paired-end sequencing was done on all samples. Raw data was presented an SAM files and BED files (only for 3 samples names Total with treatment). The SAM files were converted to BED using SAMtools and BEDtools. Resulting BED files contained only plus strand tags without information on the paired tag. Final conversion to SGA files was done using ChIP-Seq with unstranded output (-u option).

References

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 22085965

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