|
| Status |
Public on Feb 20, 2014 |
| Title |
peripheral blood_Case4_3 |
| Sample type |
RNA |
| |
|
| Source name |
peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
case/control pair: 4
age at sample (months): 24
time from seroconversion (months): 6.4
time from t1d diagnosis (months): no T1D diagnosis
gender: male
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 -70C 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 |
biotin
|
| Label protocol |
50 ng of total RNA was processed to cDNA with Nugen Ovation RNA Amplification System V2 (cat. no 3100-60) and subsequently biotin-labelled and fragmented with Nugen Encore Biotin Module (cat. no 4200-A01) according to manufacture’s protocol.
|
| |
|
| Hybridization protocol |
Samples were hybridized to GeneChip Human Genome U219 array plate with specific protocols for using the GeneTitan Hybridization, Wash and Stain Kit for 3’ IVT Array Plates (cat. no 901530).
|
| Scan protocol |
GeneTitan MC Instrument was used to hybridize, wash, stain and scan the arrays. Affymetrix GeneChip Command Console (AGCC) 3.1 was used to control GeneTitan hybridization process and in summarizing probe cell intensity data (.CEL file generation).
|
| Description |
Case4_3
|
| Data processing |
Sample T1DControl7_4 was excluded from the final analysis as an outlier. The CEL file and a readme for T1DControl7_4 containing the Metadata are provided as supplementary files on the Series record. The intensities were RMA normalized and log2-transformed using R/Bioconductor.
|
| |
|
| Submission date |
Jan 14, 2013 |
| 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 |
GPL13667 |
| Series (2) |
| GSE30211 |
Gene expression changes during Type 1 diabetes pathogenesis |
| GSE43488 |
Genome-wide expression kinetics of children with Type 1 diabetes (T1D) -associated autoantibodies or progression towards clinical T1D, compared to healthy matched controls . |
|
