|
| Status |
Public on Jul 06, 2015 |
| Title |
intensive-care unit patient [20_03_2013_B11_1225] |
| Sample type |
RNA |
| |
|
| Source name |
whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
age: 79
pneumonia diagnoses: cap
thrombocytopenia: NA
endotype_cohort: discovery
endotype_class: Mars1
mortality_event_28days: 1
time_to_event_28days: 0
icu_acquired_infection: NA
icu_acquired_infection_paired: NA
diabetes_mellitus: No_DM
abdominal_sepsis_and_controls: NA
|
| Treatment protocol |
PAXgene blood RNA tubes were left at room temperaturee to defrost (4 hours) while mixing by inversion.
|
| Growth protocol |
Whole blood was collected in PAXgene blood RNA tubes, mixed by inversion 10X and stored at -80C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated in accordance with the PAXgene blood RNA isolation (QIAGEN) procedure using the QIAcube workstation.
|
| 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.
|
| Description |
blood gene expression data from healthy subjects and critically-ill patients.
|
| 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 |
Feb 05, 2015 |
| Last update date |
Jul 12, 2018 |
| 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) |
| GSE65682 |
Genome-wide blood transcriptional profiling in critically ill patients - MARS consortium |
|
