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

Samples

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

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 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).

References

Last update: 12 Oct 2017