|
| Status |
Public on May 24, 2023 |
| Title |
TF CRISPRa screen donor 2, day 10 |
| Sample type |
SRA |
| |
|
| Source name |
CD8 T cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD8 T cells
grna library: CRISPRa TF
time point: day 10
donor: 2
|
| Treatment protocol |
CD8+CCR7+ T cells were activated with a 3:1 ratio of CD3/CD28 dynabeads to cells. 24 hours post-activation, cells were transduced with CRISPRa or CRISPRi TF gRNA lentivirus.
T cells were maintained at a concentration of 1-2e6 per mL for 10 days before scRNA-seq.
|
| 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 |
polyA RNA |
| Extraction protocol |
Transduced T cells were sorted, counted, and resuspended at 1000 cells/uL. 33,300 cells were loaded into the 10x Chromium X for a targeted recovery of 20,000 cells per donor per treatment.
Libraries were constructed according to manufacturer instructions (single cell 5’ HT v2 protocol, 10x Genomics).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
CRISPRa_D2
polyA mRNA and gRNA
10x Genomics
|
| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: hg38
Supplementary files format and content: *.tar archives include barcodes.tsv, features.tsv, and matrix.mtx files; MatrixMarket files are compatible with most single-cell RNA-seq software.
|
| |
|
| 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 |
GPL24676 |
| Series (2) |
| GSE218985 |
CRISPR-based epigenome editing screens identify transcriptional and epigenetic regulators of human CD8 T cell function [CRISPRi/a TF scRNA-seq characterization] |
| GSE218988 |
CRISPR-based epigenome editing screens identify transcriptional and epigenetic regulators of human CD8 T cell function |
|
| Relations |
| BioSample |
SAMN31927596 |
| SRA |
SRX18413848 |
