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Sample GSM2778906 Query DataSets for GSM2778906
Status Public on Feb 15, 2019
Title pre-vaccination blood sample from donor 610097 stimulated 15 hours with DMSO
Sample type RNA
 
Source name Blood sample from donor 610097
Organism Homo sapiens
Characteristics donor: 610097
post-thraw resting: no
rna extraction protocol: Micro kit
stimulation: DMSO
stimulation time: 15
stimulation time unit: hours
visit: pre
hiv infection: No
Treatment protocol Peripheral blood mononuclear cells were stimulated in vitro for 15 hours with short peptides (15-mers) of HIV-1 Env or for 15 hours with the vehicle (DMSO).
Extracted molecule total RNA
Extraction protocol RNA was isolated using the Rneasy micro kit (Qiagen) and the quality of the RNA was confirmed using a NanoDrop 2000c (Thermo Fisher Scientific) and an Experion Electrophoresis System. Samples with an RQI classification ≥7.0 were selected to proceed downstream to amplification. Samples were normalized at 50ng for input and amplified using Illumina TotalPrep RNA amplification kits (Ambion) according to the manufacturer’s protocol.
Label biotin
Label protocol The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.
 
Hybridization protocol Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol.
Scan protocol The arrays were scanned using an Illumina iScan scanner and quantified using Genome Studio software (Illumina).
Description transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d610097_pre_DMSO_15h
Data processing Raw probe intensities were preprocessed using the R (version 3.3.2) statistical language. Missing values were imputed using the KNN algorithm implemented in the R package impute (version 1.48.0). Log2 transformation was performed for variance stabilization and followed by quantile normalization as implemented in Bioconductor software package limma (version 3.30.7).
 
Submission date Sep 10, 2017
Last update date Feb 17, 2019
Contact name Slim Fourati
E-mail(s) slim.fourati@northwestern.edu
Organization name Northwestern University
Department Medicine
Lab Fourati
Street address 300 E Superior St
City Chicago
State/province Illinois
ZIP/Postal code 60611
Country USA
 
Platform ID GPL10558
Series (2)
GSE103671 Transcriptomic profiling of RV144 trial participants before and after vaccination with ALVAC-HIV and AIDSVAX B/E.[rv144pilot]
GSE103740 Transcriptomic profiling of RV144 trial participants

Data table header descriptions
ID_REF
VALUE log2-transformed and quantile normalized signal intensities.
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1343291 14.28054975 0
ILMN_1343295 11.93118616 0
ILMN_1651199 6.39126336 0.918421053
ILMN_1651209 7.072153159 0
ILMN_1651210 6.791502499 0.127631579
ILMN_1651221 6.802090111 0.114473684
ILMN_1651228 13.0370321 0
ILMN_1651229 7.587035438 0
ILMN_1651230 6.484062988 0.764473684
ILMN_1651232 6.879038187 0.040789474
ILMN_1651235 6.363960044 0.939473684
ILMN_1651236 6.510151331 0.736842105
ILMN_1651237 6.497545757 0.764473684
ILMN_1651238 6.522984609 0.717105263
ILMN_1651249 6.510151331 0.744736842
ILMN_1651253 6.573809793 0.619736842
ILMN_1651254 9.746194871 0
ILMN_1651259 7.31168564 0
ILMN_1651260 6.377942373 0.930263158
ILMN_1651262 10.87090125 0

Total number of rows: 47323

Table truncated, full table size 1536 Kbytes.




Supplementary file Size Download File type/resource
GSM2778906_5713317002_D_Grn.idat.gz 2.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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