|
| Status |
Public on Feb 20, 2014 |
| Title |
T1DCase16_9 |
| Sample type |
RNA |
| |
|
| Source name |
T1DCase16
|
| Organism |
Homo sapiens |
| Characteristics |
case/control pair: 16
age at sample (months): 45
time from seroconversion (months): 29
time from t1d diagnosis (months): -0
gender: male
tissue: peripheral blood
hla-dqb1 genotype: 0302
|
| Growth protocol |
2.5 ml of venous blood was drawn into PAXgene Blood RNA tubes (PreAnalytix Switzerland), at the Type 1 Diabetes Prediction and Prevention (DIPP) study clinic, Turku, Finland. The samples were incubated for 2 hours at RT and then stored at -70 °C until analyzed.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total whole-blood RNA was extracted from the samples using PAX gene RNA Blood RNA kit (Qiagen, Germany) according to manufacturer's instructions. RNA quality and quantity was determined using Nano Drop ND-1000 (Nano Drop Technologies, USA) and Experion Automated Electrophoresis System (Bio-Rad Laboratories, Finland).
|
| Label |
Cy3
|
| Label protocol |
100 ng total RNA was amplified to cDNA with Ovation RNA Amplification System V2 (NuGEN, cat. no 3100-60), including Ovation Whole Blood Reagent (cat. no 1300-60). The amplified cDNA was labelled according to NuGEN’s Illumina Solution protocol, Application Note #2.
|
| |
|
| Hybridization protocol |
750 ng each cDNA was hybridized to Human HT-12 Expression BeadChips, version 3 (Illumina, cat. no BD-103-0603) at 58 °C overnight (18 h) according to Illumina Whole-Genome Gene Expression Direct Hybridization protocol, revision A. Hybridizations were detected with 1 ug/ml Cyanine3-streptavidine (GE Healthcare Biosciences cat. no PA43001).
|
| Scan protocol |
Chips were scanned with Illumina Bead Array Reader, BeadScan software version 3.5. The numerical results were extracted with GenomeStudio2008 v1 without any normalization or background subtraction.
|
| Data processing |
The intensities were quantile normalized and log2-transformed using R/Bioconductor.
|
| |
|
| Submission date |
Jun 24, 2011 |
| Last update date |
Feb 20, 2014 |
| Contact name |
Henna Kallionpää |
| E-mail(s) |
[email protected]
|
| Phone |
+358-2-333-8001
|
| Organization name |
University of Turku
|
| Department |
Turku Centre for Biotechnology
|
| Lab |
Riitta Lahesmaa
|
| Street address |
P.O. Box 123
|
| City |
Turku |
| ZIP/Postal code |
FIN-20521 |
| Country |
Finland |
| |
|
| Platform ID |
GPL6947 |
| Series (2) |
| GSE30210 |
Genome-wide espression kinetics of children progressing to clinical Type 1 diabetes (T1D). |
| GSE30211 |
Gene expression changes during Type 1 diabetes pathogenesis |
|
