NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7709685 Query DataSets for GSM7709685
Status Public on Feb 26, 2024
Title CAF01*2, biol rep 2, bulk RNAseq
Sample type SRA
 
Source name Spleen
Organism Mus musculus
Characteristics tissue: Spleen
cell type: YFP+ cells
treatment: 2*CAF01: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 SAMN36982033
SRA SRX21361125

Supplementary file Size Download File type/resource
GSM7709685_18134XR-75-14V2-S13_CAF01_counts.txt.gz 151.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap