|
| Status |
Public on Feb 17, 2023 |
| Title |
Anti-PD1, NOG-EXL, scRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
PDX
|
| Organism |
Mus musculus |
| Characteristics |
tissue: PDX
cell line: patient-derived primary cancer culture
cell type: cancer cell and CD8 T cells
strain: NOG-EXL (hGM-CSF/hIL-3 NOG)
treatment: Anti-PD1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tumors were removed, processed into single cell suspension using a GentleMACS dissociator (Miltenyi Biotec) as described in the manufacturer protocol. Single cell was captured, lysed and reverse transcribed into cDNA using the 10x Chromium Single Cell V(D)J Reagent Kits and 10x Chromium controller, as described in the manufacturer protocol.
Libraries were prepared for sequencing using 10x Chromium Single Cell V(D)J Reagent Kits
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.2.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Seurat version 3.1.5 for downstream analysis
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
Feb 13, 2023 |
| Last update date |
Feb 17, 2023 |
| Contact name |
Yiqun Elaine Cao |
| Organization name |
Duke-NUS Medical School
|
| Street address |
8 College Road
|
| City |
Singapore |
| ZIP/Postal code |
169857 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE225170 |
scRNA-seq of cancer and CD8+ cells during early metastasis identifies targetable subpopulations and immune evasion mechanisms |
|
| Relations |
| BioSample |
SAMN33269953 |
| SRA |
SRX19352013 |
