|
| Status |
Public on Mar 27, 2023 |
| Title |
P2120_N701-S504 |
| Sample type |
SRA |
| |
|
| Source name |
Tetramer+ CD4+ T cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: NOD
cell type: T cell
treatment: pMHCII-NPs
|
| Treatment protocol |
Treated samples are obtained from mice that have received intravenously 10 doses of BDC2.5mi/IAg7-NPs.
Treated samples are obtained from mice that have received intravenously 10 doses of BDC2.5mi/IAg7-NPs.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single-cell sorting in SMARTseq2 plates
Smart-seq protocol (Picelli et al., 2013)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Tetramer+ CD4+ T cells from BDC 2.5mi/IAg7-NP-treated NOD mice
Raw_counts_BDC_SMARTseq2.xlsx
|
| Data processing |
Quality check with FastQC v0.11.8
Alignment to the mouse genome mm10 with STAR v2.5.4b
Gene expression estimation with RSEM v1.3.0
QC filtering of low quality cells
TCR sequences reconstructed to infer clonality with TraCeR v.0.5.1
Genome_build: mm10
Supplementary_files_format_and_content: xlsx (Raw counts for each cell)
|
| |
|
| Submission date |
May 13, 2021 |
| Last update date |
Mar 27, 2023 |
| Contact name |
Pere Santamaria |
| E-mail(s) |
pesantam@clinic.cat
|
| Organization name |
IDIBAPS
|
| Street address |
C/Rosselló 149-153
|
| City |
Barcelona |
| ZIP/Postal code |
08036 |
| Country |
Spain |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE173601 |
scRNAseq studies of pMHCII-NP-induced Tet+ cells with different epitope specificities |
|
| Relations |
| BioSample |
SAMN19165488 |
| SRA |
SRX10873734 |
