|
Status |
Public on Apr 13, 2017 |
Title |
EGFR-p14-noDrug-v2_ATAC-seq |
Sample type |
SRA |
|
|
Source name |
WM989 cell line
|
Organism |
Homo sapiens |
Characteristics |
drug tx: no drug population: EGFR-high 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 |
SAMN06711441 |
SRA |
SRX2733838 |