|
| Status |
Public on Feb 02, 2024 |
| Title |
40_S40 |
| Sample type |
SRA |
| |
|
| Source name |
Blood
|
| Organism |
Chlorocebus sabaeus |
| Characteristics |
subject: S1120-5-1
timepoint: D21
Sex: F
tissue: Blood
treatment: Vaccin
|
| Treatment protocol |
9 African green monkeys (AGM) were vaccinated with CD40.NiV+Poly-ICLC at D0 and D21
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole blood was sampled in tempus buffer (ThermoFisher Scientific). Total RNA was purified from whole blood using the Tempus Spin RNA Isolation Kit (ThermoFisher Scientific). RNA samples were depleted of globin mRNA using the Globinclear Kit (Invitrogen)
mRNA library preparation using the NEB Kit (NEBNext Biolab). Libraries were sequenced on an Illumina HiSeq 2500 V4 system.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
CD40.NiV+Poly-ICLC
|
| Data processing |
Transcript reads were aligned and quantified relative to the “Vero_WHO_p.1.0 Chlorocebus sabaeus (AGM) transcriptome reference from NCBI using Salmon v1.9.0. Quality control of the alignment was performed via MultiQC v1.1345. Finally, counts were filtered and normalized (cpm + 0,0001) using EdgeR v3.38 R package. Low expressed genes were excluded using filterByExpr function with default parameters. The conserved counts were normalized as counts per million, plus 0.0001 to avoid null values, then log2 transformed.
Differential gene expression analysis was performed with the dearseq v.1.8.4 package using a mixed model with variance component test to calculate the adjusted p values and with limma v3. package to obtain the fold-change in expression.
Assembly: Vero_WHO_p.1.0 Chlorocebus sabaeus (AGM) transcriptome reference from NCBI
Supplementary files format and content: normalized as counts per million (log2)
|
| |
|
| Submission date |
Oct 13, 2023 |
| Last update date |
Feb 02, 2024 |
| Contact name |
Cecile LEFEBVRE |
| E-mail(s) |
cecile.lefebvre@inserm.fr
|
| Organization name |
INSERM
|
| Street address |
51 Avenue du Maréchal de Lattre de Tassigny, Bât R+1 Eq16 U955
|
| City |
CRETEIL |
| ZIP/Postal code |
94010 |
| Country |
France |
| |
|
| Platform ID |
GPL18770 |
| Series (1) |
| GSE245374 |
ANTI-CD40 DENDRITIC CELL-TARGETING VACCINE INDUCES PROTECTIVE IMMUNITY AGAINST NIPAH DISEASE |
|
| Relations |
| BioSample |
SAMN37810201 |
| SRA |
SRX22090352 |
