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| Status |
Public on Mar 07, 2022 |
| Title |
041218M-TRM [ATAC-seq] |
| Sample type |
SRA |
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| Source name |
Surgically removed Ovarian Cancer tumor tissue
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| Organism |
Homo sapiens |
| Characteristics |
cancer type: HGSOC
cell type: TRM CD8+ TILs
cell type: CD8 TILs
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissue pieces from the ovarian tumors were mechanically sissociated and single cell suspensions were prepared after debris removal. B cells were sorted using anti-human CD19 antibodies.
The scRNA-Seq libraries were prepared following the protocol provided by the 10X genomics. The cDNA and ATAC-seq libraries were completed in a single bulk reaction using the 10X Genomics Chromium NextGEM Single Cell Multiome ATAC + Gene Expression Reagent Kit. 50,000 or 25,000 sequencing reads per cell for scRNA-seq or ATAC-seq libraries, respectively, were generated on dedicated Illumina NextSeq 500 sequencing runs according to the vendor protocol.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Raw sequencing reads generated from 10X multimode assay were processed by cellranger-arc workflow with default settings to generate mapping and chromatin accessibility data for ATAC and filtered UMI count data for GEX. The UMI count data for gene expression was 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 20,866 cells.
The mapping and chromatin accessibility data generated from Multiome ATAC were imported to R package Signac v1.3.0 for downstream analysis. The low-quality cells with total number of fragments in peaks < 3000 or > 20,000, fraction of fragments in peaks < 15%, ratio of mononucleosomal to nucleosome-free fragments > 4, or transcriptional start site (TSS) enrichment score < 2 were filtered out.
Genome_build: GRCH38
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
Supplementary_files_format_and_content: csv files include peaks( local enrichment of transposase cut-sites) identified from ATAC data
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| Submission date |
Dec 29, 2021 |
| 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) |
| GSE192780 |
Single-cell RNA/ATAC multiomic analysis of TRM and ReCirulating CD8+ T cells from 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 |
SAMN24502650 |
| SRA |
SRX13555728 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5765331_041218M-TRM_atac_peaks.bed.gz |
291.3 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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