|
| Status |
Public on Nov 14, 2024 |
| Title |
spleen, PDAC_64, scRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Spleen PDAC
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Spleen PDAC
treatment: Untreated
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Spleens were cut and stomached in the Stomacher 80 Biomaster. After red blood cell lysis, dead cells were removed using Dead Cell Removal MicroBeads (Miltenyi; Catalog-No.: 130-090-101).
Splenocytes were given to the UNMC Genomics Core Facility, which then prepared the scRNA-seq libraries using 10x Genomics' Chromium Single Cell Platform 3' (Version 3), following standard protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
10x Genomics
|
| Data processing |
Transcript reads were aligned to the GRCh38 Human Genome reference by the Cell Ranger 3.0.0 pipeline (10x Genomics, Inc.) to generate matrix files containing cell barcodes, UMIs (unique molecular identifiers), and transcript counts.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
Nov 13, 2023 |
| Last update date |
Nov 14, 2024 |
| Contact name |
Michael A Hollingsworth |
| Organization name |
University of Nebraska Med Center
|
| Department |
Eppley Cancer Institute
|
| Street address |
BCC 8.12.384, 601 S Saddle Creek Road
|
| City |
Omaha |
| State/province |
NE |
| ZIP/Postal code |
68106-6805 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE247635 |
Single-cell RNA-sequencing of human spleens reveals an IDO-1+ Tolerogenic Dendritic Cell subset in pancreatic cancer patients that is absent in normal individuals. |
|
| Relations |
| SRA |
SRX22293164 |
| BioSample |
SAMN38047456 |
