|
| Status |
Public on Jan 03, 2020 |
| Title |
human_endotoxemia_2ng/kg_Ecoli_LPS [19_05_2015_A12_1001224] |
| Sample type |
RNA |
| |
|
| Source name |
blood
|
| Organism |
Homo sapiens |
| Characteristics |
age: 20
gender: male
hospital: amc
subject: 1001224
timepoint pre(-)/post(+) lps: +24 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 |
|
