NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2778838 Query DataSets for GSM2778838
Status Public on Feb 15, 2019
Title post-vaccination blood sample from donor 328351 stimulated 15 hours with DMSO
Sample type RNA
 
Source name Blood sample from donor 328351
Organism Homo sapiens
Characteristics donor: 328351
post-thraw resting: no
rna extraction protocol: Micro kit
stimulation: DMSO
stimulation time: 15
stimulation time unit: hours
visit: post
treatment: RV144 vaccine
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 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d328351_post_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 14.30006519 0
ILMN_1343295 12.07461862 0
ILMN_1651199 6.605104528 0.535620053
ILMN_1651209 7.185909097 0
ILMN_1651210 6.75119491 0.208443272
ILMN_1651221 6.817748797 0.10817942
ILMN_1651228 12.94090916 0
ILMN_1651229 7.843892158 0
ILMN_1651230 6.541346082 0.68469657
ILMN_1651232 6.727252308 0.236147757
ILMN_1651235 6.474141382 0.795514512
ILMN_1651236 6.541346082 0.668865435
ILMN_1651237 6.52735707 0.713720317
ILMN_1651238 6.37493279 0.931398417
ILMN_1651249 6.63051839 0.473614776
ILMN_1651253 6.592640464 0.571240106
ILMN_1651254 9.911424156 0
ILMN_1651259 6.89853184 0.058047493
ILMN_1651260 6.432477855 0.865435356
ILMN_1651262 10.81562886 0

Total number of rows: 47323

Table truncated, full table size 1553 Kbytes.




Supplementary file Size Download File type/resource
GSM2778838_5713317004_E_Grn.idat.gz 2.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap