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Sample GSM4085615 Query DataSets for GSM4085615
Status Public on Sep 20, 2019
Title DMSO_IFNg_rep2.rpm
Sample type SRA
Source name SqCC/Y1 cells
Organism Homo sapiens
Characteristics agent: 100 ng/ul IFNg
Treatment protocol SqCC/Y1 cells were treated with either DMSO, 100 ng/ul IFNg, and/or 0.5 uM Pictilisib (GDC-0941) for 48 hours
Growth protocol SqCC/Y1 cells were grown in Dulbecco’s Modified Eagle Medium with 4.5 g/L D-glucose and L-Glutamine with 10% fetal bovine serum at 5% CO2
Extracted molecule genomic DNA
Extraction protocol 50,000 cells were centrifuged for 10 minutes at 500xg and resuspended in 25 ul of Tagmentation Reaction mix (1x TD Buffer, 2.5 ul Tn5 Transpoase, 0.2% Digitonin, 0.1% Tween-20) and incubating for 60 minutes at 37°C. DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc).
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 3000
Data processing Raw sequencing reads were mapped to the hg19 version of the human genome using Bowtie-1.1.1 with the default settings.
For each sample peaks of accessibility were identified and annotated using MACS2 with the default settings
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files are normalized to reads per million (rpm) using R/Bioconductor
Supplementary_files_format_and_content: tab delimited text file containing rpm normalized data for all peaks and all samples as well as peak annotations and locations.
Submission date Sep 19, 2019
Last update date Sep 20, 2019
Contact name Chris Scharer
Organization name Emory University
Department Microbiology and Immunology
Lab Chris Scharer
Street address 1510 Clifton Rd, Suite 3086A
City Atlanta
State/province GA
ZIP/Postal code 30322
Country USA
Platform ID GPL21290
Series (1)
GSE137719 ATAC-seq profiling assessing the impact of IFNg and Pictilisib on human SqCC/Y1 cells
BioSample SAMN12787852
SRA SRX6873174

Supplementary file Size Download File type/resource 190.8 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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