 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 03, 2024 |
| Title |
Mouse 2, pooled barcoded tissue Tregs, GEX |
| Sample type |
SRA |
| |
|
| Source name |
Blood, liver, kidney, pancreas, small intestine
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Blood, liver, kidney, pancreas, small intestine
cell type: Treg
genotype: WT
animal id: Mouse 2
library type: mRNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tregs were flow sorted on a BD Influx, Aria, Jazz or Fusion on the basis of CD4+Foxp3Thy1.1+ i.v.CD45- CD19-CD11b-CD8-F4/80-. Cells were labeled with Hashtag TotalSeq regents and loaded onto the 10x Chromium Controller. Sequencing was performed on an Illumina HiSeq.
scRNA-Seq was performed using 10x Genomics 5’ VDJ Single Cell Immune Profiling.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
10X Genomics
|
| Data processing |
The demultiplexing, barcode processing, gene counting, VDJ assembly and aggregation were performed in Cell Ranger
For TCR sequence analysis, scRNA data was used to allow for paired TCRαβ chain identification. Row sequencing data was processed with CellRanger 5.0.0 without barcode mismatches allowed and with multi-features analysis (gene expression, vdj-t, totalseq hashtags). Features were linked based on cell barcodes and tissue origin was retrieved based on hashtags signals when highest hashtag count was at least 30 times higher than the others using a custom R script. Gene expression and TCR repertoire analysis were generated in R using circlize, dplyr, ggplot2, ggsci, Matrix, pheatmap,scales, scater, Seurat, SingleCellExperiment, tidyr, viridis packages. For repertoire analysis, a TCR clonotype is associated to a unique set of Trav, tra_cdr3, trbv, trb_cdr3. The custom script is available at: https://github.com/AdrianListon/TissueTregTCR.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: CITE-Seq
|
| |
|
| Submission date |
Apr 29, 2024 |
| Last update date |
May 03, 2024 |
| Contact name |
Adrian Liston |
| E-mail(s) |
al989@cam.ac.uk
|
| Organization name |
University of Cambridge
|
| Department |
Department of Pathology
|
| Lab |
Liston-Dooley Lab
|
| Street address |
Tennis Court Road
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 1QP |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE266111 |
The tissue-resident regulatory T cell pool is shaped by transient multi-tissue migration and a conserved residency program. scRNA-Seq profiling of mouse tissue Tregs with TCR sequencing and CITE-Seq |
|
| Relations |
| BioSample |
SAMN41113778 |
| SRA |
SRX24393454 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8240880_ALFX24_1c_gex_filtered_barcodes.tsv.gz |
18.5 Kb |
(ftp)(http) |
TSV |
| GSM8240880_ALFX24_1c_gex_filtered_features.tsv.gz |
284.2 Kb |
(ftp)(http) |
TSV |
| GSM8240880_ALFX24_1c_gex_filtered_matrix.mtx.gz |
23.4 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
