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Series GSE97590 Query DataSets for GSE97590
Status Public on Aug 29, 2017
Title Next Generation Sequencing RNA Seq data from UKE Phase I rVSV ZEBOV vaccine clinical trial, from full blood samples on Days 0,1,3,7
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary 10 adult participants of dose group 3x10^6 pfu, and 10 participants of dose group 20x10^6 pfu. Reads were aligned to the human reference assembly (GRCh38.p7) using STAR software (v2.4.2a; option '--quantMode GeneCounts'). Gene annotation was obtained from Ensembl (release 79, ensemble.org). VOOM+Limma analysis (R software, version 3.2.2) was used to assess differential gene expression at each post-vaccination day (d1, d3 and d7) against baseline (d0). Next, we intergreted gene expression data and antibody response using an sPLS algorithm, in order to down-select genes correlating with multivariate antibody responses at days 28, 54, 84,180.
 
Overall design 56 samples from D0, D1, D3 and D7 were analysed. Data from samples with low RIN (RIN <8, 17 samples), low RNA or library concentration (2 samples), missing samples (5 samples) were set to missing.
 
Contributor(s) Lorenzo H, Rechtien A
Citation(s) 28854372
Submission date Apr 10, 2017
Last update date May 15, 2019
Contact name Hadrien Lorenzo
E-mail(s) hadrien.lorenzo@inria.fr
Organization name INSERM/INRIA
Department Biostatistiques
Lab SISTM
Street address 32 rue de Nerac
City Bordeaux
ZIP/Postal code 33800
Country France
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (56)
GSM2572707 Participant anonymized number 7 at day 0
GSM2572708 Participant anonymized number 7 at day 3
GSM2572709 Participant anonymized number 7 at day 7
Relations
BioProject PRJNA382377
SRA SRP103772

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE97590_counts.tsv.gz 2.4 Mb (ftp)(http) TSV
GSE97590_countsNormalized.RData.gz 6.1 Mb (ftp)(http) RDATA
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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