|
| Status |
Public on Aug 12, 2014 |
| Title |
Con063 |
| Sample type |
RNA |
| |
|
| Source name |
peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: peripheral blood
corrected gestational age (weeks+days): 44+1
gender: Male
on antibiotics at time of sample: No
bloodculture result: na
other positive results: No
birthweight (g): 3309
|
| 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 using a linear amplification method using tailed oligo dT priming of total RNA. 500ng of total RNA was used with the manual target preparation protocol from Codelink Expression Bioarray System (GE/Amersham Biosciences). Double stranded cDNA synthesis was performed with a T7oligo (dT) primer, containing a T7 RNA polymerase promoter site added to the 3’. The cDNA is used as a template for in vitro transcription with biotin labeled nucleotides and the labeled cRNA used for hybridization ( http://www.appliedmicroarrays.com/back_up/CodeLink.html ).
|
| |
|
| Hybridization protocol |
10ug of biotinylated cRNA was hybridised overnight at 37oC in 260ul hybridisation mix as described in the standard CodeLink hybridization protocol ( http://www.appliedmicroarrays.com/back_up/CodeLink.html )
|
| Scan protocol |
The bioarrays are then dried and scanned on the Agilent G2567A scanner at 5 um resolution using a standard CodeLink scanning protocol ( http://www.appliedmicroarrays.com/back_up/CodeLink.html ).
|
| Description |
Platform Test Set
|
| Data processing |
Raw data were obtained from the scanned images using CodeLinkTM EXPv4.1 (GE Healthcare) feature extraction software. Subsequent data validation comprising data quality control and normalisation involved the use of the statistical software package R/Bioconductor. Raw scan data were background subtracted and subsequently normalised using the Robust Multi-array Average (RMA) method.
|
| |
|
| Submission date |
Jun 04, 2014 |
| Last update date |
Jun 14, 2016 |
| 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 |
GPL15158 |
| Series (1) |
| GSE25504 |
Whole blood mRNA expression profiling of host molecular networks in neonatal sepsis |
|
