|
| Status |
Public on May 22, 2018 |
| Title |
Kelly ATAC [Lab: Look] |
| Sample type |
SRA |
| |
|
| Source name |
Neuroblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Kelly
|
| Growth protocol |
Cells were cultured according to the suggested guidelines in RPMI media containing 10% FBS and 1% Penicillin-Streptomycin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were generated using the Ad1 and Ad2.13–2.24 barcoded primers from and were amplified for 7–9 total cycles
DNA was simultaneously fragmented and tagged with sequencing adapters using the Nextera Tn5 transpoase kit
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw reads were separately aligned using bowtie with parameters --sam --best -k 1 -m 1 -l 75
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1
|
| |
|
| Submission date |
Feb 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard A Young |
| E-mail(s) |
young_computation@wi.mit.edu
|
| Phone |
617-258-5219
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Lab |
Young Lab
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE94823 |
Super-enhancer Driven Core Regulatory Circuitry in MYCN-amplified Neuroblastoma [ATAC-Seq] |
| GSE94824 |
Super-enhancer Driven Core Regulatory Circuitry in MYCN-amplified Neuroblastoma |
|
| Relations |
| BioSample |
SAMN06324669 |
| SRA |
SRX2555312 |
