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Sample GSM7709691 Query DataSets for GSM7709691
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 ( 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 ( 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
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
BioSample SAMN36982050
SRA SRX21357220

Supplementary file Size Download File type/resource
GSM7709691_C_DBEC_MolsPerCell_Unfiltered.csv.gz 23.5 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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