|
| Status |
Public on Jan 11, 2024 |
| Title |
scRNA-Seq_TCRb+_Tcells_DTx2 |
| Sample type |
SRA |
| |
|
| Source name |
T cells from tumors
|
| Organism |
Mus musculus |
| Characteristics |
tissue: T cells from tumors
cell type: TCR-b+ T cells
genotype: Foxp3-EGFP-DTR
treatment: DTx
|
| Treatment protocol |
Animals were administered PBS or DTx as indicated
|
| Growth protocol |
Syngeneic B16-F10 melanoma cells were subcutaneously implanted into Foxp3EGFP-DTR mice and ablated Treg cells through administration of DTx. T cells were isolated by FACS and subjected to RNA-Seq analysis
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single-cell suspensions were purified by FACS-sorting of total TCR-b+ T cells from tumors of PBS- or DTx-treated Foxp3-EGFP-DTR animals. Cell suspensions were subjected to scRNA-Seq using the Chromium 10x scRNA-Seq platform
Chromium 10x scRNA-Seq 5’ library preparation with TCR enrichment was performed according to manufacturer's instructions
Samples were individually barcoded according to Chromium 10x 5' kit instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Cells were isolated by fluorescence-activated cell sorting and subjected to sc-RNA-Seq using the Chromium 10x scRNA-Seq platform, barcoded and sequenced
|
| Data processing |
Chromium 10x libraries were demultiplexed and subjected to Chromium cellranger analysis as per manufacturer instructions
Cellranger gene expression profiles were analysed using Seurat
Assembly: mm9
Supplementary files format and content: tab-delimited text files include normalised gene expression values
|
| |
|
| Submission date |
Jul 07, 2023 |
| Last update date |
Jan 11, 2024 |
| Contact name |
Rahul Roychoudhuri |
| E-mail(s) |
rr257@cam.ac.uk
|
| Organization name |
University of Cambridge
|
| Department |
Department of Pathology
|
| Lab |
Roychoudhuri Laboratory
|
| Street address |
Tennis Court Road
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 1QP |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE236824 |
Acquisition of suppressive function by CD4+ conventional T cells limits anti-tumor immunity driven by Treg depletion [scRNA-seq] |
| GSE236825 |
Acquisition of suppressive function by CD4+ conventional T cells limits anti-tumor immunity driven by Treg depletion. |
|
| Relations |
| BioSample |
SAMN36359254 |
| SRA |
SRX20951794 |
