|
| Status |
Public on Aug 03, 2023 |
| Title |
tonsil tissue-KD-GEX |
| Sample type |
SRA |
| |
|
| Source name |
tonsil from Tonsilitis patients
|
| Organism |
Homo sapiens |
| Characteristics |
condition: Tonsilitis
tissue: tonsil
cell line: Primary cells
cell type: Sorted CD4 Tconv and Tregs
genotype: Wild Type
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single-cell suspensions from tonsil tissues and tumors were generated by mechanical disruption followed by enzymatic digestion in serum-free Roswell Park Memorial Institute media (RPMI). After initial isolation from tissue, cells were passed through a 100 μm filter and spun down to yield single-cell suspensions. Cells were stained and sorted for live CD4+ Tconv (CD4+CD25-CD127high) and Tregs (CD4+CD25highCD127low) by fluorescence-activated cell sorting (FACS) on the Sony MA900 at the Hillman Cancer Center Cytometry Facility.
Immediately following sorting, Tconv and Tregs were centrifuged for 5 min at 500 xg and were resuspended in PBS with 0.04% BSA. Cells were then counted using the Cellometer Auto2000 (Nexcelom) and loaded into the 10X Controller (10X Genomics) targeting a recovery of 2000 cells per sample. The RNA capture, barcoding, cDNA and library preparation were performed according to the manufacturer’s recommendations (single cell 3' v2).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
GEX
|
| Data processing |
scRNA-seq
CellRanger (10X Genomics, version 3.1.0) pipeline to generate gene/barcode matrices.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-separated files and matrix file
|
| |
|
| Submission date |
Aug 01, 2023 |
| Last update date |
Aug 03, 2023 |
| Contact name |
Feng Shan |
| E-mail(s) |
shf43@pitt.edu
|
| Phone |
4126943757
|
| Organization name |
University of Pittsburgh
|
| Street address |
Ford Building, 5051 Centre Ave
|
| City |
Pittsburgh |
| State/province |
Pennsylvania |
| ZIP/Postal code |
15213 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE239750 |
Integrated BATF transcriptional network regulates suppressive intratumoral regulatory T cells |
|
| Relations |
| BioSample |
SAMN36780985 |
| SRA |
SRX21206972 |
