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Sample GSM2575291 Query DataSets for GSM2575291
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

Supplementary file Size Download File type/resource
GSM2575291_EGFR-p14-noDrug-v2.bedGraph.gz 52.4 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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