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| Status |
Public on Mar 07, 2022 |
| Title |
T041218-TRM-VDJ |
| Sample type |
SRA |
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| Source name |
Surgically removed High Grade Serous Ovarian Cancer tumor tissue
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| Organism |
Homo sapiens |
| Characteristics |
cancer type: HGSOC
cell type: TRM CD8+ TILs
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| 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.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
CD8 TILs
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| 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
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| Submission date |
Jan 20, 2022 |
| Last update date |
Mar 07, 2022 |
| Contact name |
jiqiang yao |
| Organization name |
moffitt cancer center
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| Street address |
12902 USF Magnolia Drive
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| City |
Tampa |
| ZIP/Postal code |
33612 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN25144946 |
| SRA |
SRX13849577 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5828148_T041218-TRM_filtered_contig_annotations.csv.gz |
635.6 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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