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| Status |
Public on Jun 06, 2017 |
| Title |
S2 T0 rep1 traditional occupancy |
| Sample type |
SRA |
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| Source name |
UPR-induced S2 cells, T0, traditional occupancy
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: S2 cell
time: T0 (0 hours, control)
mnase concentration: 1.5U, 6.25U, 25U and 100U MNase titrations pooled before sequencing
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
[MNase-seq] MNase titration was performed as described previously (Mieczkowski, Cook, Bowman et al. Nat. Communications 2016). For h-MACC, after addition of EDTA/EGTA and SDS half of the digests were kept at 4C as input, the other half were adjusted to ChIP buffer conditions [10mM TRIS ph8.0, 100mM NaCl, 1mM EDTA, 0.1% sodiumdeoxycholate, 0.5% sarkosyl, 1% triton x-100 and complete protease inhibitors (Roche)] with 1ml of ChIP buffer. After tumbling for 10min at 4C, the digests were spun at high speed for 10min at 4C and the supernatant was incubated with anti H3 antibodies (abcam ab1791) as described (Bowman et al. BMC Genomics 2013).
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| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| 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) |
tolstorukov@molbio.mgh.harvard.edu
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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 |
SAMN06478035 |
| SRA |
SRX2612494 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2521720_T0.trad.nucs.occ.r1.bedgraph.gz |
78.2 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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