|
| Status |
Public on Jan 11, 2024 |
| Title |
CD4_Tumor_DTx_2 |
| Sample type |
SRA |
| |
|
| Source name |
Tumour-infiltrating T cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Tumour-infiltrating T cells
cell type: CD4+ Tconv cell
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 |
total RNA |
| Extraction protocol |
Single-cell suspensions were purified by total CD4+ T cell enrichment followed by FACS-sorting stored in 40 µl RNAlater™ Stabilization Solution at -80 °C Samples were processed using the QIAshredder Kit (Qiagen) according to the manufacturer’s protocol RNA was extracted from samples using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s protocol RNA Libraries were prepared using the SmartSeq2 protocol on an automated Hamilton NGS-STAR library preparation system and sequenced using a Illumina sequencing instrument
SmartSeq2, Samples were individually barcoded
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Cells were isolated by fluorescence-activated cell sorting and stored in 40 µl RNAlater™ Stabilization Solution at -80 °C Samples were processed using the QIAshredder Kit (Qiagen) according to the manufacturer’s protocol RNA was extracted from samples using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA Libraries were prepared using the SmartSeq2 protocol on an automated Hamilton NGS-STAR library preparation system and sequenced using a HiSeq instrument
|
| Data processing |
FastQ files underwent quality control with FastQC, adaptor trimming with Cutadapt and alignment to the NCBIM37 Mus musculus genome annotation. Count tables containing genic read counts were normalised using intergenic read density as background for subtraction
Differential gene expression analysis was performed using DESeq2 and differentially expressed genes were futher analysed using R
Assembly: Genome_build: mm9
Supplementary files format and content: Supplementary_files_format_and_content: tab-delimited text files include FPM values
|
| |
|
| Submission date |
Jul 12, 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 |
GPL13112 |
| Series (2) |
| GSE236825 |
Acquisition of suppressive function by CD4+ conventional T cells limits anti-tumor immunity driven by Treg depletion. |
| GSE237140 |
Acquisition of suppressive function by CD4+ conventional T cells limits anti-tumor immunity driven by Treg depletion [RNA-seq II] |
|
| Relations |
| BioSample |
SAMN36416238 |
| SRA |
SRX20994043 |
