|
| Status |
Public on Oct 14, 2024 |
| Title |
RNA-Seq S4_sgFlcn_day4.5 |
| Sample type |
SRA |
| |
|
| Source name |
sgFlcn-transduced OT-1 cells purified from the siIEL on day 4.5 post-LM-OVA infection
|
| Organism |
Mus musculus |
| Characteristics |
cell type: sgRNA transduced OT-1 cells
strain: C57BL/6
|
| Growth protocol |
sgNTC or sgFlcn-transduced OT-1 cells purified from the siIEL on days 4.5 and 7.5 post-LM-OVA infection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CD8+ OT1 T cells were 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 |
| |
|
| Description |
sgFlcn_OT-1_day4.5
|
| 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 |
May 02, 2023 |
| Last update date |
Oct 14, 2024 |
| 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) |
| GSE231495 |
Interplay between nutrient stress and lysosomal signaling imprints immune memory in tissues [scRNAseq] |
| GSE231502 |
CRISPR screens unveil nutrient-dependent lysosomal and mitochondrial nodes impacting intestinal tissue-resident memory CD8+ T cell formation |
|
| Relations |
| BioSample |
SAMN34535827 |
| SRA |
SRX20189959 |
