|
| Status |
Public on Nov 10, 2020 |
| Title |
M4_TCR_day10_LCMV_armstrong |
| Sample type |
SRA |
| |
|
| Source name |
CD4
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6 mice
infection: LCMV armstrong
tissue: spleen
|
| Treatment protocol |
Activated antigen specific CD4 T cells (CD4+CD44+GP66+) were sorted from five C57BL/6J mice at day 10 post acute LCMV armstrong infection and were loaded on the Chromium Controller (10x Genomics). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 5’ v2 and v3 Reagent Kit (10x Genomics) according to manufacturer’s protocol. Libraries were loaded onto an Illumina NextSeq with the NextSeq 500/550 High Output Kit v2 (150 cycles)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Chromium single cell 5' kit V2 from 10x genomics
Chromium single cell 5' kit V2 from 10x genomics for single cell gene expression (GEX) and single cell TCR library
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Day 10 LCMV armstrong
|
| Data processing |
Reads were aligned to mouse reference genome mm10
Single cell TCR data were filtered to select the best TCR alpha and beta chain at the clonal level, based on full length, productive CDR3 regions and expression level
Genome_build: mm10
Supplementary_files_format_and_content: Matrix files were generated using Cell Ranger (10x Genomics).
|
| |
|
| Submission date |
Oct 01, 2020 |
| Last update date |
Nov 11, 2020 |
| Contact name |
Weiguo Cui |
| E-mail(s) |
[email protected]
|
| Phone |
312-503-0332
|
| Organization name |
Northwestern University
|
| Department |
Pathology
|
| Lab |
Cui
|
| Street address |
303 E Chicago Ave
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60654 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE158896 |
Single-cell lineage mapping of a diverse virus-specific naïve CD4 T cell repertoire |
|
| Relations |
| BioSample |
SAMN16337167 |
| SRA |
SRX9232261 |
