|
| Status |
Public on Feb 20, 2014 |
| Title |
peripheral blood-Case8_1 |
| Sample type |
RNA |
| |
|
| Source name |
peripheral blood-Case8
|
| Organism |
Homo sapiens |
| Characteristics |
case/control pair: 8
age at sample (months): 17
time from seroconversion (months): -11.9
time from t1d diagnosis (months): no T1D diagnosis
gender: male
tissue: peripheral blood
hla-dqb1 genotype: 02, 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 of total RNA was amplified and reverse transcribed with Ovation RNA amplification system v2 (NuGEN, cat. no 3100-60), including Ovation whole blood reagent (cat. no 1300-60). 5 ug cDNA was labeled according to NuGEN’s Illumina solution protocol, application note #2. cDNA concentration and quality was controlled with Experion Automated Electrophoresis System (Bio-Rad Laboratories, Finland).
|
| |
|
| Hybridization protocol |
1.5 ug each sample was hybridized to Illumina Sentrix Human-6 V2 Expression Bead Chips 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. Numerical results were extracted with Bead Studio v3.3without 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) |
henna.kallionpaa@btk.fi
|
| 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 |
GPL6102 |
| Series (2) |
| GSE30209 |
Genome-wide expression kinetics of children with T1D-associated autoantibodies compared to healthy matched controls II |
| GSE30211 |
Gene expression changes during Type 1 diabetes pathogenesis |
|
