|
| Status |
Public on Jun 06, 2017 |
| Title |
S2 T4 ATAC-seq rep2 |
| Sample type |
SRA |
| |
|
| Source name |
UPR-induced S2 cells, T4 ATAC-seq
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: S2 cell
time: T4 (4 hours)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
[ATAC-seq] 5x10^4 S2 cells from each time point were collected and washed in cold PBS. ATAC-Seq libraries were prepared as described previously (Buenrostro et al. Nat. Methods 2013; Buenrostro et al. Curr Protoc Mol Biol. 2015). Briefly, cells were resuspended in cold lysis buffer and centrifuged to collect nuclei. Transposition reaction was performed for 30 minutes at 37°C using Tn5 transposase from Nextera. DNA fragments were purified using a Minelute kit (Qiagen). DNA fragments were amplified using Nextera barcoded primers as described. Amplified library was purified with SPRI beads. Paired End 50 sequencing was done on an Illumina HiSeq2000 according to manufacturer’s instructions.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| 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
|
| |
|
| Submission date |
Mar 04, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Tolstorukov |
| E-mail(s) |
tolstorukov@molbio.mgh.harvard.edu
|
| Organization name |
Massachusetts General Hospital
|
| Department |
Molecular Biology
|
| Street address |
185 Cambridge Street
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE95689 |
Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction |
|
| Relations |
| BioSample |
SAMN06478024 |
| SRA |
SRX2612505 |
