|
| Status |
Public on Nov 20, 2018 |
| Title |
d10_Tet |
| Sample type |
SRA |
| |
|
| Source name |
CD8+ TIL
|
| Organism |
Mus musculus |
| Characteristics |
cell type: SIINFEKL Tetramer+ CD8+ T cells isolated from B16-OVA melanoma tumors day 10 after implantation
strain: C57BL/6
isolation of cd45+ cells from tumors: CD8+ MACS positive selection (Miltenyi) followed by FACS
|
| Treatment protocol |
Mice were not treated
|
| Growth protocol |
3 x 10^5 B16-OVA tumor cells were injected subcutaneously into C57BL/6 mice. On day 10 or 20 after implantation, tumors were extracted and processed as noted below
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tumors were dissected from the surrounding fascia, mechanically minced and treated with collagenase P and DNAse I for 10 minutes at 37C. Tumor-infiltrating leukocytes were enriched using Optiprep (Sigma) density gradient followed by CD8+ MACS positive selection (Miltenyi) and FACS isolation. Cells were counted and loaded onto the 10x device (10x Genomics).
Library construction was performed as per standard 10x protocol (Manual CG00052 Rev B)
10X single-cell 3' RNA-seq v2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting, and aggregation of multiple sequencing runs were performed using the Cell Ranger analysis pipeline (v1.2)
Data normalization, dimension reduction, and differential expression analysis were performed using the Seurat R package (v2.2.0)
Single cell signatures scoring was performed using the FastProject software (v1.1.0)
Genome_build: mm10
Supplementary_files_format_and_content: matrix.mtx file is count matrix in sparse matrix format; barcodes.tsv is list of barcodes for each sample; genes.tsv is list of genes detected in samples
|
| |
|
| Submission date |
Nov 19, 2018 |
| Last update date |
Nov 20, 2018 |
| Contact name |
Kevin Bi |
| E-mail(s) |
[email protected]
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Pediatric Oncology
|
| Lab |
Haining Lab
|
| Street address |
450 Brookline Ave.
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215-5450 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE122675 |
10X single-cell RNASeq profiling of tumor-infiltrating CD8+ T-cells from B16-OVA mouse melanoma tumors |
| GSE122713 |
scRNA-seq, bulk RNA-seq, and ATAC-seq data from progenitor exhausted and terminally exhausted CD8+ T cells from tumors and chronic viral infection |
|
| Relations |
| BioSample |
SAMN10440640 |
| SRA |
SRX5025642 |
