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Sample GSM2911162 Query DataSets for GSM2911162
Status Public on Jan 03, 2020
Title human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_H11_100262]
Sample type RNA
 
Source name blood
Organism Homo sapiens
Characteristics age: 23
gender: male
hospital: amc
subject: 100262
timepoint pre(-)/post(+) lps: +2 hours
stem cell dose: placebo
Treatment protocol none
Growth protocol PAXgene blood
Extracted molecule total RNA
Extraction protocol Total RNA was isolated by means of the QIAcube machine (Qiagen, Venlo, the Netherlands) in combination with the PAXgene Blood mRNA kit (Qiagen) according to manufacturer’s instructions.
Label biotin
Label protocol 100ng total RNA was labeled using standard GeneChip® 3' IVT Express Kit (Affymetrix)
 
Hybridization protocol Standard Affymetrix GeneAtlas® Hybridization, Wash, and Stain Kit.
Scan protocol Standard GeneTitan® multi channel instrument.
Data processing Raw data scans (.CEL files) were read into the R language and environment for statistical computing (version 2.15.1; R Foundation for Statistical Computing, Vienna, Austria; http://www.R-project.org/). Pre-processing and quality control was performed by using the Affy package version 1.36.1. Array data were background corrected by Robust Multi-array Average, quantiles-normalized and summarized by medianpolish using the expresso function. The resultant 49,386 probe intensities were filtered by means of a 0.5 variance cutoff using the genefilter method to recover 24,646 expressed probes. The occurrence of non-experimental chip effects was evaluated by means of the Surrogate Variable Analysis (R package version 3.4.0) and corrected by the empirical Bayes method ComBat.
 
Submission date Jan 03, 2018
Last update date Jan 03, 2020
Contact name Brendon Scicluna
E-mail(s) brendon.scicluna@um.edu.mt
Organization name University of Malta
Street address Msida campus
City Msida
ZIP/Postal code MSD2020
Country Malta
 
Platform ID GPL13667
Series (1)
GSE108685 Genome-wide blood transcriptional profiling in human endotoxemia given human adipose-derived mesenchymal stem cells

Data table header descriptions
ID_REF
VALUE Normalized and log2 transformed values

Data table
ID_REF VALUE
11715101_s_at 3.151384935
11715103_x_at 3.390654382
11715110_at 5.950775854
11715111_s_at 4.904324071
11715122_at 4.815036681
11715124_s_at 3.874210244
11715125_at 4.971928921
11715126_s_at 3.660221686
11715129_s_at 4.890403162
11715130_s_at 2.95306708
11715135_s_at 3.216179748
11715137_s_at 3.09813989
11715138_s_at 5.131639092
11715140_s_at 2.650810534
11715150_s_at 4.029160139
11715155_s_at 3.832453719
11715156_s_at 7.140592538
11715159_at 7.892801628
11715161_s_at 2.304837767
11715162_s_at 2.907777985

Total number of rows: 24646

Table truncated, full table size 614 Kbytes.




Supplementary file Size Download File type/resource
GSM2911162_29_04_2015_H11_100262.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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