|
| Status |
Public on Apr 13, 2017 |
| Title |
neg-p9-week4_ATAC-seq |
| Sample type |
SRA |
| |
|
| Source name |
WM989 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
drug tx: week 4
population: EGFR-negative
cell line: WM989
cell type: melanoma
|
| Treatment protocol |
We treated cells with 1uM vemurafenib.
|
| Growth protocol |
We grew melanoma cell lines (WM989 and WM983B) from the lab of Meenhard Herlyn in Tu2% media containing 78% MCDB, 20% Leibovitz’s L-15 media, 2% FBS, and 1.68mM CaCl2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
We performed ATAC sequencing on WM989-A6 melanoma cells according to Buenrostro et al. Briefly, we lysed the cells and set up the transposition reaction with the Tn5 Transposes (Illumina Catalog #FC121-1030) at 37℃ for 30 minutes. We cleaned the reaction with a Qiagen MinElute Kit and then amplified the libraries using custom Nextera PCR primers.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ATAC-sequencing
|
| Data processing |
We aligned our reads to hg19 with bowtie2
HOMER package for peak calling, differential peak calling, motif analysis, and gene ontology analysis
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph format
|
| |
|
| Submission date |
Apr 12, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Sydney M Shaffer |
| E-mail(s) |
sydshaffer@gmail.com
|
| Organization name |
University of Pennsylvania
|
| Street address |
BRB II/III, Room 445, 421 Curie Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE97680 |
Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance [ATAC-seq] |
| GSE97682 |
Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance |
|
| Relations |
| BioSample |
SAMN06711449 |
| SRA |
SRX2733849 |
