NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6761477 Query DataSets for GSM6761477
Status Public on May 24, 2023
Title CD8 T cells, GFP control, acute, donor 2, day 14
Sample type SRA
 
Source name CD8 T cells
Organism Homo sapiens
Characteristics cell type: CD8 T cells
genotype: GFP control
condition: acute stimulation
time point: day 14
donor: 2
Growth protocol CD8 T cells were cultured in PRIME-XV T cell expansion XSFM (FujiFilm) supplemented with 5% human platelet lysate (Compass Biomed), 100 units/mL of penicillin, 100 units/mL of streptomycin, and 100 units/mL human IL-2 (Peprotech).
Extracted molecule genomic DNA
Extraction protocol 50,000 transduced CD8 T cells were sorted for ATAC-seq.
ATAC-seq libraries were prepared according to the Omni ATAC-seq protocol.
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model NextSeq 2000
 
Description CD8_Tcell_GFP_acute_D2
Data processing Read quality was assessed with FastQC and adapters were trimmed with Trimmomatic.
Trimmed reads were aligned to the hg38 reference genome using Bowtie (v1.0.0) using parameters -v 2 --best --strata -m 1.
Reads mapping to the ENCODE hg38 blacklisted regions were removed using bedtools2 intersect (v2.25.0).
Duplicate reads were excluded using Picard MarkDuplicates (v1.130).
Count per million normalized bigWig files were generated for visualization using deeptools bamCoverage (v3.0.1).
Peak calling was performed using MACS2 narrowPeak and filtered for an adjusted P value < 0.001.
Peak calls were merged across samples to make a union-peak set. A count matrix containing the number of reads in peaks for each sample was generated using feature Counts (subread v1.4.6) and used for differential analysis in DESeq2.
Assembly: hg38
Supplementary files format and content: NarrowPeak files with peak information and signal.
Supplementary files format and content: bigWig files normalized by library size.
 
Submission date Nov 29, 2022
Last update date May 24, 2023
Contact name Sean McCutcheon
E-mail(s) sean.mccutcheon@duke.edu
Phone 7073447178
Organization name Duke University
Department Biomedical Engineering
Lab Charles Gersbach
Street address 101 Science Drive, CIEMAS Rm. 2323
City Durham
State/province NC
ZIP/Postal code 27708
Country USA
 
Platform ID GPL30173
Series (2)
GSE218987 CRISPR-based epigenome editing screens identify transcriptional and epigenetic regulators of human CD8 T cell function [ATAC-seq]
GSE218988 CRISPR-based epigenome editing screens identify transcriptional and epigenetic regulators of human CD8 T cell function
Relations
BioSample SAMN31927054
SRA SRX18413375

Supplementary file Size Download File type/resource
GSM6761477_SCM-69-rep2.masked.dedup.sorted.rpkm.bw 187.2 Mb (ftp)(http) BW
GSM6761477_SCM-69-rep2.masked.dedup.sorted_peaks.narrowPeak.gz 1.8 Mb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap