|
| Status |
Public on Nov 15, 2023 |
| Title |
"spike for sgEts1_1"_ day 7 2 |
| Sample type |
SRA |
| |
|
| Source name |
sgRNA transduced OT-I cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: sgRNA transduced OT-I cells
transduced: sgNTC (‘spike for sgEts1’)
strain: C57BL/6
|
| Growth protocol |
OT-I cells transduced with indicatd sgRNAs were sorted from B16-OVA tumor after adoptive transfer
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CD8+ OT-I T cells were sorted from the dual-color transfer system 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 and Gel Bead Kit (10x Genomics)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| 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 barcode processing to generate gene-cell matrices used for downstream analysis.
Assembly: mm10
Supplementary files format and content: cell ranger count matrix for single cells in each sample
|
| |
|
| Submission date |
Nov 19, 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 |
| GSE218372 |
Single-cell CRISPR screens in vivo map T cell fate regulomes in cancer [Ets1 scRNAseq] |
|
| Relations |
| BioSample |
SAMN31800321 |
| SRA |
SRX18319181 |
