|
| Status |
Public on May 22, 2023 |
| Title |
T99 |
| Sample type |
SRA |
| |
|
| Source name |
scRNA-seq on MCC tumor resected from lymph node of a treatment naïve male patient
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Merkel cell carcinoma tumor
tissue: Resected tumor from lymph node
mcpyv status: MCPyV positive
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Resected patient tumors were dissociated followed by red blood cell lysis, washed, and passed through 22µm sterile filters to obtain single-cell suspensions. Dead cells were excluded by SYTOX staining and live cells were collected by the FACSAria Fusion flow cytometer (BD Biosciences) and BD FACSDiva (v8.0.1). Sorted cells were washed with PBS containing 0.04% BSA and resuspended at a final density of ~1000 cells/µL.
Libraries were created targeting ~10,000 cells/sample for capture using Chromium Single Cell 3’ Reagent Kits following the CG00052 Rev B. user guide. Each library was subsequently sequenced on the Illumina NovaSeq 6000 platform to targeting an average of ~50,000 reads/cell.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x Genomics Cloud Analysis platform (https://www.10xgenomics.com/products/cloud-analysis). FASTQ files were aligned to GRCh38 human reference genome using Cell Ranger Count v6.1.2. The number of average mapped reads per cell across the libraries were thereafter normalized using Cell Ranger Aggr function. Output files from Cell Ranger were imported to R and analyzed further using Seurat.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
Mar 01, 2023 |
| Last update date |
May 22, 2023 |
| Contact name |
Ling Gao |
| E-mail(s) |
ling.gao@va.gov, lingg3@hs.uci.edu
|
| Organization name |
Department of Veterans Affairs
|
| Street address |
5901 E.7th Street
|
| City |
Long Beach |
| State/province |
California |
| ZIP/Postal code |
90822 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE226438 |
Single cell RNA-seq profiling of patient-derived Merkel cell carcinoma tumor samples |
|
| Relations |
| BioSample |
SAMN33559682 |
| SRA |
SRX19542874 |
