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Sample GSM5828155 Query DataSets for GSM5828155
Status Public on Mar 07, 2022
Title T082219-TRM-VDJ
Sample type SRA
 
Source name Surgically removed High Grade Serous Ovarian Cancer tumor tissue
Organism Homo sapiens
Characteristics cancer type: HGSOC
cell type: TRM CD8+ TILs
Extracted molecule total RNA
Extraction protocol Tissue pieces from the ovarian tumors were mechanically dissociated and single cell suspensions were prepared after debris removal. TRM and re-circulating CD8+ TILs were FACs sorted in Aria-sort
The scRNA-Seq libraries were prepared following the protocol provided by the 10X genomics. The cDNA and VDJ-enriched libraries were completed in a single bulk reaction using the 10X Genomics Chromium NextGEM Single Cell 5’ v 1.1 and V(D)J Reagent Kits. 50,000 or 5,000 sequencing reads per cell for scRNA-seq or VDJ libraries, respectively, were generated on the Illumina NextSeq 500 instrument.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NextSeq 500
 
Description CD8 TILs
Data processing Library strategy: TCR-seq
Raw sequencing reads from scRNA-seq were processed using Cell Ranger (v3.0, 10X Genomics). Cell barcodes and UMIs associated with the aligned reads were subjected to correction and filtering. Filtered gene-barcodes matrices containing only barcodes with UMI counts passing threshold for cell detection were imported to Seurat v4.0 for downstream analysis.
Barcodes with fewer than 200 genes expressed, or more than 10% UMIs originated from mitochondrial genes, were excluded filtered out; genes expressed in fewer than 3 barcodes were also excluded. This process resulted in 43,368 cells for TRM+re-circ scRNA-seq from 4 tumors, and 60,010 cells for TRM scRNA-seq from 8 tumors.
TCR reads sequenced by V(D)J assay were aligned to GRCh38 reference transcriptome using Cell Ranger VDJ. T cells were assigned with productive CDR3 regions for TCR alpha and TCR beta chains.
Each clonotype was assigned with a unique identifier based on amino acid sequences of the CDR3 regions and V(D)J genes of the two chains, which was then used to match clonotypes across samples
Genome_build: GRCH38
Supplementary_files_format_and_content: csv files include assembled TCR heavy chain and light chain sequences and VDJ annotation for each T cell
Supplementary_files_format_and_content: csv files include the number of UMIs associated with a gene (row) and a cell (column) measured from single-cell RNA-seq
 
Submission date Jan 20, 2022
Last update date Mar 07, 2022
Contact name jiqiang yao
Organization name moffitt cancer center
Street address 12902 USF Magnolia Drive
City Tampa
ZIP/Postal code 33612
Country USA
 
Platform ID GPL18573
Series (2)
GSE194105 single-cell RNA and TCR sequencing of TRM CD8+ T cells sorted from 8 HGSOC tumors
GSE195486 Ovarian cancer immunogenicity is governed by a narrow subset of progenitor tissue-resident memory T-cells
Relations
BioSample SAMN25144939
SRA SRX13849584

Supplementary file Size Download File type/resource
GSM5828155_T082219-TRM_filtered_contig_annotations.csv.gz 169.4 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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