|
| Status |
Public on Apr 16, 2024 |
| Title |
(2) rhIL-7-hyFc [TCR] |
| Sample type |
SRA |
| |
|
| Source name |
Tumor
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Tumor
cell line: MC38
cell type: CD8 T cell
genotype: Wild type
strain: C57BL/6
treatment: rhIL-7-hyFc (1.25mpk, s.c.)
|
| Treatment protocol |
(Condition 1) C57BL/6 mice bearing palpable MC38 tumors were treated s.c. with rhIL-7-hyFc (10 mg kg-1). Tumors were collected 7 days after the rhIL-7-hyFc treatment for scRNA-seq/scTCR-seq analyses of TILs. (Condition 2) C57BL/6 mice bearing palpable MC38 tumors given rhIL-7-hyFc (1.25 mg kg-1) were treated i.v. with anti-mPD-L1 anti-CD3ε TCE 3 times daily 3 days after rhIL-7-hyFc treatment. Tumors were collected 24 hours after the last treatment for scRNA-seq analyses of TILs
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were euthanized at indicated time points and tumor tissues were harvested. Tumor tissues were mechanically dissected and then digested with collagenase D (400 units/mL; Roche) and DNase I (200 ug/mL; Roche) in washing buffer (2% NCS plus Antibiotic-Antimycotic in RPMI-1640) for 30 min in a shaking incubator at 37 °C. The enzyme-digested tumor meshed over a 70-um cell strainer. Red blood cells (RBC) were lysed with RBC lysing buffer (Sigma-Aldrich). For the enrichment of CD8 T cells, cells were isolated by positive selection methods with IMag according to the manufacturer’s protocol (condition 1) or sorted by FACS (GhostDyeCD45+TCRb+CD8a+) (condition 2) after single-cell preparation. The purified CD8 T cells were analyzed by scRNA-seq paired with scTCR-seq.
Chromium Next GEM Single Cell 5p RNA library v2 for gene expression and Chromium Next GEM Single Cell VDJ library v2 for TCR seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
10X Genomics
|
| Data processing |
The 10x Genomics Cell Ranger, version (1) 4.0.0 or (2) 6.1.2 was used to align reads and count the single-cell sequencing data using the GRCm38 as the reference genome: ‘cell ranger count’ and ‘cell ranger vdj’ pipelines were applied to process scRNA-seq and TCR-seq, respectively, that led to generating feature, barcode, and matrices for (1) treatment with either buffer or rhIL-7-hyFc or (2) treatment with either rhIL-7-hyFc or a combination of rhIL-7-hyFc and TCE.
Assembly: GRCm38
Supplementary files format and content: Cell Ranger outs are compressed with gzip
|
| |
|
| Submission date |
Jul 13, 2023 |
| Last update date |
Apr 17, 2024 |
| Contact name |
Hawon Song |
| Organization name |
Kangwon National University
|
| Street address |
Gangwon Daehak-gil 1
|
| City |
Chuncheon |
| ZIP/Postal code |
24341 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE237266 |
IL-7-primed bystander CD8 tumor-infiltrating lymphocytes optimize the antitumor efficacy of T-cell engager immunotherapy in solid tumors |
|
| Relations |
| BioSample |
SAMN36436038 |
| SRA |
SRX21011301 |
