|
| Status |
Public on Feb 25, 2021 |
| Title |
"spike for sgPofut1_2"_ day 7 |
| Sample type |
SRA |
| |
|
| Source name |
sgRNA-transduced P14 cells from the dual-color transfer system at day 7 post-infection from spleen
|
| Organism |
Mus musculus |
| Characteristics |
cell type: sgRNA transduced P14 cells
strain: C57BL/6
genotype/variation: spike for sgPofut1
|
| Growth protocol |
P14 cells transduced with indicated sgRNAs were sorted from spleen after LCMV-Armstrong infection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CD8+ T cells were sorted from sgRNA transduced P14 cells from the dual-color transfer system at day 7 post-infection from spleen 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 |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
The Cell Ranger 1.3 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.
Genome_build: mm10
Supplementary_files_format_and_content: cell ranger count matrix for single cells in each sample
|
| |
|
| Submission date |
Oct 28, 2020 |
| Last update date |
Feb 27, 2021 |
| 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) |
| GSE160305 |
In vivo CRISPR screening reveals nutrient signaling processes underpinning CD8+ T cell fate decisions [scRNA-seq] |
| GSE160341 |
In vivo CRISPR screening reveals nutrient signaling processes underpinning CD8+ T cell fate decisions |
|
| Relations |
| BioSample |
SAMN16581321 |
| SRA |
SRX9388899 |
