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Series GSE46734 Query DataSets for GSE46734
Status Public on May 22, 2015
Title DALIA-1 Whole Blood Longitudinal Gene Expression
Organism Homo sapiens
Experiment type Expression profiling by array
Summary The DALIA-1 trial was designed to evaluate the safety and immunogenicity of a DC-based vaccine generated by culturing blood monocytes with GM-CSF and IFN-a. DCs were pulsed for 24 hrs with the ANRS LIPO5 peptide pool and activated for the last 6 hrs with LPS. In total, 19 asymptomatic HAART-treated patients were included in the study. Microarray samples were collected in both the treatment phase and follow-up phase of the study.
 
Overall design Whole blood RNA samples were collected at two time points prior to the first vaccination (Weeks -8 and -4) and served as a pre-vaccination baseline. Additional whole blood RNA samples were collected at the time of vaccination (Weeks 0, 4, 8, 12) and post-vaccination at weeks 16, 22, and 24. At week 24, an analytical treatment interruption (ATI) was initiated during which HAART was suspended. During this post-ATI follow-up phase, whole blood RNA samples were collected at weeks 25, 26, 27, 28, 32, 36, 40, , 44, and 48). Additionally, at weeks -4, 16, and 48 patients were apheresed. 18 samples are constituents of both the pre-ATI and post-ATI datasets, which were normalized separately.

The normalised data underwent the following preprocessing:
First a normal-exponential convolution model was applied (Xie et al, Bioinformatics, 2009; Shi et al, Nucleid Acids Research, 2010) to correct for the background noise. An offset of 16 (default value) was then added to the data (to improve precision and avoid a compression of the fold changes) before a quantile-quantile normalization was performed. Finally, data were log2 transformed. Only probes whose pval-detection (provided by Illumina Genome-Studio software) was below 0.01 in at least one sample were kept further on. At last, the ComBat method (Johnson et al, Biostatistics, 2007) was applied to those data in order to correct for batch effects (namely a small hybridization chamber effect, that was identified through Principal Variance Component Analysis - Li et al, chap. 12, Batch Effects and Noise in Microarray Experiments: Sources and Solutions, Wiley, 2009).
 
Contributor(s) Skinner JA, Hejblum BP, Thiébaut R
Citation(s) 31105698
Submission date May 08, 2013
Last update date May 29, 2019
Contact name Jason A Skinner
E-mail(s) jaskinner06@yahoo.com
Organization name Baylor Institute for Immunology Research
Street address 3434 Live Oak
City Dallas
State/province TX
ZIP/Postal code 75204
Country USA
 
Platforms (1)
GPL10558 Illumina HumanHT-12 V4.0 expression beadchip
Samples (330)
GSM1136304 P6_22, pre-ATI
GSM1136305 P11_8
GSM1136306 P9_4
Relations
BioProject PRJNA202208

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
GSE46734_DALIA1longitudinalTranscriptome_DESIGN_anonym.txt.gz 2.2 Kb (ftp)(http) TXT
GSE46734_DALIA1longitudinalTranscriptome_PALO01_PostATI_NEQC_NonParamCombat.txt.gz 45.8 Mb (ftp)(http) TXT
GSE46734_DALIA1longitudinalTranscriptome_PALO01_PreATI_NEQC_NonParamCombat.txt.gz 35.6 Mb (ftp)(http) TXT
GSE46734_DALIA1longitudinalTranscriptome_RawDataFromGenomeStudio_ControlProbes.txt.gz 3.2 Mb (ftp)(http) TXT
GSE46734_DALIA1longitudinalTranscriptome_RawDataFromGenomeStudio_RegularProbes.txt.gz 166.0 Mb (ftp)(http) TXT
GSE46734_RAW.tar 26.2 Mb (http)(custom) TAR
GSE46734_README.txt 1.2 Kb (ftp)(http) TXT
GSE46734_non-normalized_post-ATI.txt.gz 52.5 Mb (ftp)(http) TXT
GSE46734_non-normalized_pre-ATI.txt.gz 40.6 Mb (ftp)(http) TXT
Processed data included within Sample table
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