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Status |
Public on Jan 03, 2020 |
Title |
human_endotoxemia_2ng/kg_Ecoli_LPS [29_04_2015_F11_100196] |
Sample type |
RNA |
|
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Source name |
blood
|
Organism |
Homo sapiens |
Characteristics |
age: 23 gender: male hospital: amc subject: 100196 timepoint pre(-)/post(+) lps: +6 hours stem cell dose: medium
|
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)
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|
|
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.
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|
|
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 |
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