|
| Status |
Public on Apr 24, 2018 |
| Title |
ATAC_N+RIS_Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
IMR90
|
| Organism |
Homo sapiens |
| Characteristics |
vector 1: ER:HRAS(G12V)
vector 2: pWZL N1ICD
4oht: Yes
passage: 23-28
|
| Treatment protocol |
For RIS samples, cells are treated for 6 days with 4OHT. For co-cultures, IMR90 ER:HRAS(G12V) cells expressing mRFP are cultured for 6 days in the presence of 4OHT before flow sorting of red cells.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq performed using 100,00 cells and 13 cycles of PCR amplification. Otherwise, as previously described (Buenrostro et al., 2015).
Libraries prepared using 13 cycles of PCR following nuclei transposition using the Nextera DNA library preperation kit (Illumina, FC-121-1030). Samples were size selected between 170 and 400bp (in order to isolate ‘nucleosome free’ and ‘mono-nucleosome’ fragments) using SPRIselect beads (B23319, Beckman Coulter)
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Mapped to the human reference (hg19) with BWA (version 0.7.12)
Low quality reads (mapping quality less than 20) as well as known adapter contamination were filtered out using Cutadapt (version 1.10.0)
Average fragment size was determined using the ChIPQC Bioconductor package, and peak calling was performed with MACS2 (version 2.1.0), using fragment size as an extension size (--extsize parameter)
Coverage files were generated using MACS2 (version 2.1.0).
Genome_build: hg19
Supplementary_files_format_and_content: .bedgraph = coverage files
Supplementary_files_format_and_content: .narrowPeak = peak files
|
| |
|
| Submission date |
Sep 07, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Shamith Samarajiwa |
| Organization name |
Imperial College London
|
| Department |
Genetics and Genomics Section Department of Metabolism, Digestion and Reproduction
|
| Lab |
Computational Biology & Data Science
|
| Street address |
ICTEM Building, Hammersmith Campus, Du Cane Road,
|
| City |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE103588 |
NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence [ATAC-Seq] |
| GSE103590 |
NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence |
|
| Relations |
| BioSample |
SAMN07614492 |
| SRA |
SRX3167007 |
