|
| Status |
Public on Feb 26, 2024 |
| Title |
CAF01*2 + CAF16*4, scRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Spleen
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Spleen
cell type: YFP+ cells
treatment: 2*CAF01:H56 + 4*CAF16:H56 s.c.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells from the spleen of IL-17A fate reporter mice immunized with either CAF01:H56 two times with two weeks in between (n = 10) or followed by four immunizations with CAF16:H56 were processed and stimulated with H56 (1 µg/ml) for 6 hours at 37 oC. Next, CD4+ T cells were isolated using the EasySep mouse CD4+ T cell isolation kit (STEMCELL Technologies Inc., Canada) according to the manufacturer’s recommendation. Live YFP+ cells were sorted using a BD FACSAria™ Cell Sorter (BD BioSciences).
Cells were prepared for sequencing using the BD Rhapsody™ Immune Response Panel Mm (Cat.no: 633753, 397 genes, BD BioSciences) and the BD Rhapsody™ Scanner (BD BioSciences) according to the manufacture’s recommendations.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
BD Rhapsody™ Immune Response Panel Mm (Cat.no: 633753, 397 genes, BD BioSciences)
|
| Data processing |
BCL files were converted to FASTQ files with bcl2fastq (Illumina) and data were then processed with the use of BD Rhapsody™ Targeted Analysis Pipeline aligning to the mm10 genome using SevenBridges Genomics.
The raw transcript count matrix was loaded into R (v4.2.3) and the R-package Seurat (v.4.3.0) was used for analysis
Assembly: mm10
Supplementary files format and content: Csv and fastq
|
| |
|
| Submission date |
Aug 14, 2023 |
| Last update date |
Feb 26, 2024 |
| Contact name |
Katharina Wørzner |
| E-mail(s) |
kawo@ssi.dk
|
| Organization name |
Statens Serum Institut
|
| Department |
Infectious Disease Immunology
|
| Street address |
Artillerivej 5
|
| City |
Copenhagen |
| ZIP/Postal code |
2300 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE240801 |
F2833 scRNA-seq data for manuscript "Therapeutic vaccine containing a novel liposomal adjuvant shifts pathogenic Th17 cells into a Tr1-like phenotype" |
| GSE240802 |
Repeated Immunization with ATRA-containing Liposomal Adjuvant Transdifferentiates Th17 Cells to a Tr1-like Phenotype |
|
| Relations |
| BioSample |
SAMN36982050 |
| SRA |
SRX21357220 |
