|
| Status |
Public on May 26, 2022 |
| Title |
Expt 2 M1 left tumor GEX |
| Sample type |
SRA |
| |
|
| Source name |
MC-38 tumor
|
| Organism |
Mus |
| Characteristics |
tissue: MC-38 tumor
cell type: CD8+ tumor infiltrating T cells
independent experiment: 2
mouse id: 4
tumor: left tumor
|
| Growth protocol |
1 million CD8+ T cells were injected into Rag1-/- mice on day 6. 9 days later, tumor infiltrating T cells were isolated for perturb-seq.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Direct capture perturb-seq was performed using the 10X Genomics 5' scRNA-seq kit and protocol with additional spike-in primer to capture sgRNAs in each single cell.
10X Genomics 5' scRNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
polyA RNA
|
| Data processing |
Publicly available 10X Genomics cellranger count pipeline was used to jointly process the sgRNA and gene expression libraries for each sample.
Counts matrices were loaded into Seurat for downstream processing.
Low quality barcodes were filtered out.
sgRNA counts matrix was filtered and used to assign sgRNAs to the majority of single cells.
Clustering was performed to identify cell types.
Assembly: mm10
Supplementary files format and content: Seurat object (Seurat v4) with relevant metadata (ie, sgRNA assignments and clusters).
|
| |
|
| Submission date |
May 23, 2022 |
| Last update date |
May 26, 2022 |
| Contact name |
Julia Belk |
| Organization name |
Stanford University
|
| Street address |
450 Serra Mall
|
| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL31136 |
| Series (2) |
| GSE203592 |
Genome-wide CRISPR screens of T cell exhaustion identify chromatin remodeling factors that limit T cell persistence [Perturb-seq] |
| GSE203593 |
Genome-wide CRISPR screens of T cell exhaustion identify chromatin remodeling factors that limit T cell persistence |
|
| Relations |
| BioSample |
SAMN28597908 |
| SRA |
SRX15417988 |
