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| Status |
Public on Jun 06, 2017 |
| Title |
S2 T0 Pol-II input rep1 |
| Sample type |
SRA |
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| Source name |
UPR-induced S2 cells, T0 Pol-II input
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: S2 cell
time: T0 (0 hours, control)
chip antibody: none
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| Extracted molecule |
genomic DNA |
| Extraction 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
MNase-seq, ATAC-seq and ChIP-seq: The sequenced paired-end reads were mapped to dm3 genome using Bowtie aligner v. 0.12.939. Only uniquely mapped reads with no more than two mismatches were retained. The reads with the insert sizes less than 50 bp or larger than 500 bp were filtered out. Genomic positions with the numbers of mapped tags above the significance threshold of z-score = 7 were identified as anomalous, and the tags mapped to such positions were discarded. Read frequencies were computed in 300-bp non-overlapping bins in the case of fly data and in 500-bp bins in the case of human data for each titration point independently. The read frequencies were normalized by the corresponding library sizes to represent values per one million of mapped reads. To facilitate the comparison of the results between different genomes, the frequencies were additionally scaled by the factors representing ratios between the corresponding genome size and 100 Mb.
RNA-seq: Tags were aligned using Tophat software package with default parameters. RNA-Seq tag frequencies were normalized for GC-content using bioconductor package EDASeq and then the expression estimates for each gene were obtained using bioconductor package DESeq.
Genome_build: dm3
Supplementary_files_format_and_content: bedGraph files representing coverage profiles normalized to library sizes
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| Submission date |
Mar 04, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Tolstorukov |
| E-mail(s) |
[email protected]
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| Organization name |
Massachusetts General Hospital
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| Department |
Molecular Biology
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| Street address |
185 Cambridge Street
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
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| Platform ID |
GPL13304 |
| Series (1) |
| GSE95689 |
Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction |
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| Relations |
| BioSample |
SAMN06478007 |
| SRA |
SRX2612523 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2521749_T0.Pol2.input.r1.bedgraph.gz |
78.4 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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