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SRX2612508: GSM2521734: S2 T1 H3K27ac ChIP rep1; Drosophila melanogaster; ChIP-Seq
1 ILLUMINA (Illumina HiSeq 2000) run: 26.8M spots, 2.7G bases, 1.8Gb downloads

Submitted by: NCBI (GEO)
Study: Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction
show Abstracthide Abstract
Activation of transcription requires alteration of chromatin by complexes that increase the accessibility of nucleosomal DNA. Removing nucleosomes from regulatory sequences has been proposed to play a significant role in activation. We tested whether changes in nucleosome occupancy occurred on the set of genes that are activated by the unfolded protein response (UPR). We observed no decrease in occupancy on most promoters, gene bodies, and enhancers. Instead there was an increase in the accessibility of nucleosomes, as measured by MNase digestion and by ATAC-seq, that did not result from removal of the nucleosome. Thus changes in nucleosome accessibility predominate over changes in nucleosome occupancy during rapid transcriptional induction during the UPR. Overall design: Time series of nucleosome occupancy, MNase-seq, ATAC-seq, H3K27ac, RNAseq and Pol2 profiles for UPR-induced S2 cells.
Sample: S2 T1 H3K27ac ChIP rep1
SAMN06478021 • SRS2023116 • All experiments • All runs
Library:
Instrument: Illumina HiSeq 2000
Strategy: ChIP-Seq
Source: GENOMIC
Selection: ChIP
Layout: PAIRED
Construction protocol: [H3K27ac and RNA Polymerase II protocol] 3-6 x 10^7 crosslinked cells from each treatment group were resuspended in sonication buffer (0.5% SDS, 20mM Tris pH8.0, 0.5 mM EGTA, 2mM EDTA and protease inhibitor tablets (Roche)) in a ratio of 100ul cold sonication buffer to 1x10^7 cells. Cells were lysed on ice for 10min. Cell lysates were sonicated in a Qsonica at 4C. After a hard spin for 10 min at 4C, the supernatants corresponding to 2.5 million cells were removed and either flash frozen and kept at -80 (as input) or diluted into 1ml of ChIP buffer (0.5% Triton X-100, 2mM EDTA, 20mM TRIS pH8.0, 150mM NaCl, 10% glycerol) to be used for chromatin IP after a hard spin for 10min at 4C. The IP solution was incubated with selected IP antibody at 4C overnight tumbling. The next day proteinA dynabeads (Life Technologies) were added and after a 2hr incubation while tumbling at 4C, the IP samples were washed once with low salt wash buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris pH8, 150mM NaCl), three times with high salt wash buffer (same as previous buffer but with 500mM NaCl), and once with LiCl wash buffer (0.25M LiCl, 1% NP-40, 1% NADeoxycholate, 1mM EDTA, 10mM Tris pH 8). The beads were rinsed with TE buffer and the proteins were eluted with 500ul elution buffer (1%SDS, 0.1M NaHCO3) for 30 min at room temperature. At this point the input samples were also taken up in elution buffer.
Experiment attributes:
GEO Accession: GSM2521734
Links:
Runs: 1 run, 26.8M spots, 2.7G bases, 1.8Gb
Run# of Spots# of BasesSizePublished
SRR531268326,805,0472.7G1.8Gb2017-06-07

ID:
3782367

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