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Sample GSM8022761

Query DataSets for GSM8022761

Status

Public on Mar 29, 2024

Title

CCB105, YF-17D vaccination, day 3, rep 1

Sample type

SRA

Source name

Whole blood

Organism

Macaca fascicularis

Characteristics

tissue: Whole blood
animal id: CCB105
treatment: YF-17D Vaccination
time: day 3
Sex: male

Treatment protocol

Live, attenuated YF-17D-204 vaccine (monodose Stamaril®, Sanofi)

Growth protocol

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

CCC021J3_S3_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