|
| Status |
Public on Nov 08, 2021 |
| Title |
3_TCR_GFP_m2 |
| Sample type |
SRA |
| |
|
| Source name |
Large intestinal T cells
|
| Organism |
Mus musculus |
| Characteristics |
host strain: RAG2 KO
cell type: Large intestinal T cells
cell subtype: regulatory T cell
|
| Treatment protocol |
2 RAG2 KO mice received naive CD4+ FoxP3- T cells and CD4+ FoxP3+ regulatory T cells in an adoptive T cell transfer. 7 weeks later, large intestinal FoxP3- and FoxP3+ were isolated by FACS and scTCR-Profiles were prepared
|
| Growth protocol |
-
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
T cells were FACS sorted and library preparation was performed accroding to the 10X Chromium Next GEM Single Cell V(D)J Reagent Kit v1.1 for murine T cells
DNA libraries were prepared for sequencing using the 10X Chromium Next GEM Single Cell V(D)J Reagent Kit v1.1 for murine T cells
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
3_TCR_S7
|
| Data processing |
library strategy: scTCR seq
We performed two sequencing runs, therefore each sample hast two pairs of fastq files ending with 001 and 002.
Using CellRanger analysis pipeline (v6.0) from 10x Genomics, we performed the multi-modal analysis of gene expression and TCR data simultaneously.
The pipeline workflow includes the following steps:
(1) alignment to the murine genome reference sequence,
(2) cell inference,
(3) saturation analysis and
(4) various QC metrics. Only cells tagged with 'high_confidence', 'productive' and 'full_length' were
Genome_build: GRCm38 (pre-processed release refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0 - downloaded from the website of 10x Genomics)
Supplementary_files_format_and_content: two csv for each; the first is for the annotated contigs in each cell and the other a summary table for the clonotypes.
|
| |
|
| Submission date |
Aug 09, 2021 |
| Last update date |
Nov 08, 2021 |
| Contact name |
Ali T Abdallah |
| E-mail(s) |
bioinformatics.ali.abdallah@gmail.com
|
| Organization name |
University of Cologne
|
| Department |
Medical Faculty
|
| Lab |
CECAD
|
| Street address |
Joseph Stelzmann Str. 26
|
| City |
Cologne |
| ZIP/Postal code |
50931 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE181681 |
Shaping of T cell repertoire and function in murine intestine |
|
| Relations |
| BioSample |
SAMN20669417 |
| SRA |
SRX11675985 |
