|
Status |
Public on Jun 28, 2018 |
Title |
BC10_TUMOR1_TCR |
Sample type |
SRA |
|
|
Source name |
CD3+ leukocytes
|
Organism |
Homo sapiens |
Characteristics |
donor: BC10 cell type: CD3+ leukocytes donor age (years): 73 resident tissue: breast tumor
|
Extracted molecule |
total RNA |
Extraction protocol |
Chromium Single Cell V(D)J Enrichment Kit, Human T Cell CD3+ cells from tumor were isolated by mincing the freshly obtained surgical specimens into 1 mm cubic pieces and subsequent enzymatic digestion using LiberaseTL (Sigma) for 20 min at 37°C. The digested tissues were then passed through a 100M filter and washed twice with PBS prior to surface staining. Immune cells were stained at 1x10^6 cells per ml for 20 min with anti-CD45 and DAPI for live-dead discrimination following Fc receptor blockade (BioLegend). Viable immune cells (CD45+DAPI-) were sorted on a FACSARIA sorter (BD Biosciences).
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
Contains RNA sequencing of the T-cell receptor of individual cells
|
Data processing |
10x Data was processed with the Cell Ranger pipeline, version 2.1.1 Genome_build: Gencode GRCh38 Supplementary_files_format_and_content: Cell x gene unnormalized count matrices
|
|
|
Submission date |
May 21, 2018 |
Last update date |
Jun 28, 2018 |
Contact name |
Ambrose J Carr |
Organization name |
Memorial Sloan Kettering Cancer Center
|
Department |
Computational and Systems Biology Program, SKI
|
Lab |
Dana Pe'er
|
Street address |
417 E 68th St
|
City |
New York |
State/province |
NY |
ZIP/Postal code |
10065 |
Country |
USA |
|
|
Platform ID |
GPL16791 |
Series (2) |
GSE114724 |
Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment - 5' RNA sequencing and TCR sequencing |
GSE114727 |
Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment |
|
Relations |
BioSample |
SAMN09233249 |
SRA |
SRX4108611 |