|
| Status |
Public on May 24, 2023 |
| Title |
PBS treatment GEX2 |
| Sample type |
SRA |
| |
|
| Source name |
Tumor
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Sorted CD45- tumour cells, macrophages (CD45+CD64+), CD45+ non-macrophage immune cells (CD45+CD64-), and dendritic cells (CD45+CD64-CD11c+MHC-II+) in the tumour tissues
strain: C57BL/6
agent: PBS
|
| Treatment protocol |
Wild-type mice were challenged with MC38 colon adenocarcinoma cells, and treated with PBS or glutamine daily starting from day 5. Anti-PD-1 antibody or rat IgG2b isotype control was injected intraperitoneally three times on day 7, 10 and 13.
|
| Growth protocol |
8-week-old WT mice were used
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CD45- tumour cells, macrophages (CD45+CD64+), CD45+ non-macrophage immune cells (CD45+CD64-), and dendritic cells (CD45+CD64-CD11c+MHC-II+) were sorted from tumour tissues
Libraries were prepared using the Chromium Single Cell Immune Profiling v2 Library and Gel Bead Kit (10x Genomics)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| 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 for scRNAseq and filtered contig annotations for scTCR-seq
|
| |
|
| Submission date |
Jul 31, 2022 |
| Last update date |
May 24, 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 |
GPL24247 |
| Series (2) |
| GSE210154 |
SLC38A2 and glutamine signaling in cDC1 dictate anti-tumor immunity [scRNA-Seq 2] |
| GSE210155 |
SLC38A2 and glutamine signaling in cDC1 dictate anti-tumor immunity |
|
| Relations |
| BioSample |
SAMN30072446 |
| SRA |
SRX16744415 |
