NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM8022730 Query DataSets for GSM8022730
Status Public on Mar 29, 2024
Title CCC046, YF-17D vaccination, day 1, rep 1
Sample type SRA
 
Source name Whole blood
Organism Macaca fascicularis
Characteristics tissue: Whole blood
animal id: CCC046
treatment: YF-17D Vaccination
time: day 1
Sex: male
Treatment protocol Live, attenuated YF-17D-204 vaccine (monodose Stamaril®, Sanofi)
Growth protocol NA
Extracted molecule polyA RNA
Extraction protocol Whole blood from cynomolgus macaques was collected in PAXgene tubes (BD762165 –Ozyme), and stored according to the manufacturer's protocol. RNA was extracted with the PAXgene 96 Blood RNA kit (Qiagen-762331) according to manufacturer’s instructions on Tecan Evo150 workstation. The RNA quantity, purity and quality were checked on the Labchip (Caliper) and the Nanodrop Spectrophotometer (Thermo Scientific).
Extracted RNA samples with an A260/A280 ratio ~2, a RIN>8 and a minimal concentration of 70ng/µL of RNA were processed using the GLOBINclear™-Human kit (ThermoFisher - AM1980) for the depletion of the alpha and beta globin mRNA according to manufacturer’s instructions. The quantity, purity and quality of the RNA depleted of globin mRNA was reassessed as already described before library preparation for sequencing. Sequencing libraries were prepared with the TruSeq mRNA stranded kit (Illumina - 20162122/20146602) using 300ng of RNA according to manufacturer’s instructions. The quality, length distribution and quantity of the resulting libraries were analyzed with the Qubit 3.0 Fluorometer (Life Technologies) and the Labchip (Caliper). Libraries were pooled at equimolar amounts and sequenced by single reads of 75bp on high-output flowcell (Illumina – FC-404-2005) using the Nextseq500 sequencer (Illumina) in a batch of 10 samples per flowcell with the specification to achieve 30 million reads per sample. On run completion, libraries were demultiplexed, adapters trimmed and FASTQ files generated.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description CCB072J1_S5_R1_001
Data processing A read quality check was performed on raw data in FASTQ format using FastQC (v0.11.2).
Reads were imported and then processed in OmicSoft Array Studio software (v9.0.6.38-v9.0.8.28).
The raw data QC wizard of Array Studio was executed on the reads to assess the read quality.
The reads were aligned with OmicsSoft Aligner (OSA4; (53)) in Array Studio against the Cyno.WashU2013 reference genome using WashUGene20140620 gene annotations, including a first step of read trim per quality score (minimum of 2).
Samples (CCB102J-21, CCA100J1, CCB102J1, CCA100J14, CCA100J-21, CA100J7, CCA100J3, CCB102J3, CCA100J28) that did not meet quality criteria based on the minimal number of reads sequenced underwent a second run, and files were merged after read alignment, i.e. at the BAM file level.
Naïve read count quantification was performed with the Array Studio software using WashUGene20140620 gene annotations (In Array Studio, “Naïve” means that no EM algorithm was used to handle ambiguous reads). Multiple mapping reads and first-read-forward-strand reads were discarded from the analysis (i.e. “Exclude multi-reads” option selected, “Count First-Read-Forward-Strand reads” option unselected).
Assembly: Cyno.WashU2013
Supplementary files format and content: raw_counts.txt raw counts per sample and gene (WashUGene20140620 gene annotations)
Supplementary files format and content: Count_Annotation.txt (annotation file from OmicSoft, https://qiagen.my.salesforce-sites.com/KnowledgeBase/KnowledgeNavigatorPage?id=kA46N0000008OqZSAU&categoryName=OmicSoft_Suite)
 
Submission date Jan 18, 2024
Last update date Mar 29, 2024
Contact name Emilie Chautard
E-mail(s) emilie.chautard@sanofi.com
Organization name Sanofi
Street address 1541 Avenue Marcel Mérieux
City Marcy L'Etoile
ZIP/Postal code 69280
Country France
 
Platform ID GPL22523
Series (1)
GSE253538 Cynomolgus macaques as a translational model of human immune responses to yellow fever 17D vaccination
Relations
BioSample SAMN39485037
SRA SRX23275078

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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