|
| Status |
Public on May 24, 2023 |
| Title |
CD8 T cells, GFP control, chronic, donor 1, day 14 |
| Sample type |
SRA |
| |
|
| Source name |
CD8 T cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD8 T cells
genotype: GFP control
condition: chronic stimulation
time point: day 14
donor: 1
|
| 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_chronic_D1
|
| 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 |
SAMN31927049 |
| SRA |
SRX18413380 |
