|
| Status |
Public on Nov 15, 2023 |
| Title |
sgRNA Library-transduced OT-I cells B1S2 |
| Sample type |
SRA |
| |
|
| Source name |
sgRNA Library-transduced OT-I cells at day 7 post adoptive transfer from B16-OVA tumor
|
| Organism |
Mus musculus |
| Characteristics |
cell type: sgRNA Library transduced OT-I cells
strain: C57BL/6
|
| Growth protocol |
OT-I cells transduced with indicatd sgRNA Library were sorted from B16-OVA tumor after adoptive transfer
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CD8+ OT-I T cells were sorted at day 7 post adoptive transfer from B16-OVA tumor and loaded onto the Chromium Controller according to their respective cell counts to target 9000 single cell GEMs (gel beads in emulsion) per sample.
Libraries were prepared using the Chromium Single Cell 3’ v3 Library, CRISPR screening library and Gel Bead Kit (10x Genomics)
scRNA-seq and direct capture CRISPR
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
sgRNA Library-transduced OT-I cells
|
| Data processing |
The Cell Ranger 6.0 Single-Cell Software Suite (10x Genomics) was implemented to process the raw sequencing data from the Illumina HiSeq run.
This pipeline performed de-multiplexing, alignment (mm10 and CRISPR library), and barcode processing to generate gene-cell and sgRNA-cell matrices used for downstream analysis.
Assembly: mm10
Supplementary files format and content: cell ranger gene expression and sgRNA count matrix for single cells in each sample
|
| |
|
| Submission date |
Oct 31, 2022 |
| Last update date |
Nov 15, 2023 |
| Contact name |
Hongbo Chi |
| E-mail(s) |
hongbo.chi@stjude.org
|
| Organization name |
St Jude Children's Research Hospital
|
| Department |
Immunology
|
| Street address |
262 Danny Thomas Place
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE216800 |
Single-cell CRISPR screens in vivo map T cell fate regulomes in cancer |
| GSE216909 |
Single-cell CRISPR screens in vivo map T cell fate regulomes in cancer [scCRISPR] |
|
| Relations |
| BioSample |
SAMN31535992 |
| SRA |
SRX18089645 |
