|
| Status |
Public on Feb 26, 2024 |
| Title |
CAF01*2 + CAF16*4, biol rep 2, 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 |
RNA was extracted from the cell samples using RNeasy Micro Kit (Qiagen). RNA sample quality was assessed by High Sensitivity RNA Tapestation (Agilent Technologies Inc., California, USA) and quantified by Qubit 2.0 RNA HS assay (ThermoFisher, Massachusetts, USA).
The SMART-Seq v4 ultra-low input kit was used to synthesize cDNA. Library construction was performed based on the manufacturer’s recommendation for Nextera XT kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw reads were validated using fastQC (v0.11.9) and trimmed using AdapterRemoval (v2.3.1), with a Phred score of 20 and a minimum length of 30bp.
The reads were mapped to the mouse genome (GCR 000001635.26 GRCm38.p6) using hisat2 (v2.1.0), and the read count was produced using HTSeq (v0.9.1).
The raw read counts were filtered with a threshold of 10 and normalized by rlog to construct the principle component analysis.
Assembly: mm10
Supplementary files format and content: text files includes raw counts for each sample
|
| |
|
| 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) |
| GSE240800 |
F2702 bulk RNA-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 |
SAMN36982030 |
| SRA |
SRX21361128 |
