|
| Status |
Public on Aug 12, 2014 |
| Title |
Inf012 |
| Sample type |
RNA |
| |
|
| Source name |
peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: peripheral blood
corrected gestational age (weeks+days): 34+6
gender: Female
on antibiotics at time of sample: No
bloodculture result: negative
other positive results: CSF: enterovirus on PCR. CSF also grew coag neg staph, CSF WCC 300, RBC 9
birthweight (g): 2150
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from whole blood samples with PAXgene blood RNA reagent, followed by clean-up and DNase I treatment with QIAGEN PAXgene blood RNA kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared with the standard Affymetrix GeneChip IVT labeling kit.
|
| |
|
| Hybridization protocol |
Standard Affymetrix hybridisation and wash procedure EukGE-WS2v5.
|
| Scan protocol |
GeneChips were scanned using the Affymetrx GeneChip Scanner 3000 HR using the GCOS software tool
|
| Description |
Validation Test Set
|
| Data processing |
R/Bioconductor using RMA normalisation, filtered for single present or marginal calls and empirical Bayes statistical test with Benjamini-Hochberg FDR adjustment performed for analysis of differential gene expression.
|
| |
|
| Submission date |
Jun 04, 2014 |
| Last update date |
Nov 30, 2020 |
| Contact name |
Peter Ghazal |
| E-mail(s) |
ghazalp@cardiff.ac.uk
|
| Organization name |
Cardiff University
|
| Department |
Systems Immunity University Research Institute
|
| Street address |
Sir Geraint Evans Building, Academic Avenue
|
| City |
Cardiff |
| ZIP/Postal code |
CF14 4XN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE25504 |
Whole blood mRNA expression profiling of host molecular networks in neonatal sepsis |
|
| Relations |
| Reanalyzed by |
GSE162329 |
