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Sample GSM3148582 Query DataSets for GSM3148582
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 1​x​10^6 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

Supplementary file Size Download File type/resource
GSM3148582_BC10_TUMOR1_filtered_contig_annotations.csv.gz 585.6 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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