|
| Status |
Public on Jun 01, 2013 |
| Title |
BN1 PBMCs, DR50 plasma |
| Sample type |
RNA |
| |
|
| Source name |
Brown Norway PBMCs stimulated with DR+/+ day 50 plasma
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Brown Norway (BN)
gender: male
age: ~180 days
responder cells: Brown Norway PBMCs
stimulated with: DR+/+ day 50 plasma
|
| Treatment protocol |
Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 20% autologous BN (self-baseline control), allogeneic BN (healthy-unrelated control), DRlyp/lyp, or DR+/+ plasma. Cultures were prepared in a Costar 24-well plate (Corning) using 500,000 cells/well and in RPMI 1640 medium supplemented with 100U/ml penicillin and 100ug/ml streptomycin in a total of 500 µl. After culture total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).
|
| Growth protocol |
Fresh PBMCs of healthy Brown Norway (BN) rats (~180 days old males, to avoid variation introduced by estrous or pubertal status) were isolated by density gradient centrifugation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
|
| Label |
biotin
|
| Label protocol |
cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.
|
| |
|
| Hybridization protocol |
The Affymetrix GeneChip rat genome RD230 plus 2.0 array was selected for these studies for its overall comprehensive coverage.
|
| Scan protocol |
After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner
|
| Description |
DR50 OnBN1c C59
|
| Data processing |
Image data were normalized and analyzed Partek Genomic Suite (v.6.5 (6.11.0321)) to determine signal log ratios. Each sample was independently analyzed (1 array for each time point/condition for 24 arrays; +9 arrays for BN allogenaic challenges). This time series data was analysis by S.T.E.M. - Short Time-series Expression Miner.
|
| |
|
| Submission date |
Aug 30, 2012 |
| Last update date |
Jun 01, 2013 |
| Contact name |
Martin Hessner |
| E-mail(s) |
mhessner@mcw.edu
|
| Organization name |
Medical College of Wisconsin
|
| Department |
Pediatrics
|
| Lab |
Max McGee National Research Center for Juvenile Diabetes
|
| Street address |
8701 Watertown Plank Road
|
| City |
Milwaukee |
| State/province |
WI |
| ZIP/Postal code |
53226 |
| Country |
USA |
| |
|
| Platform ID |
GPL1355 |
| Series (2) |
| GSE40497 |
Temporal induction of immunoregulatory processes coincides with age-dependent resistance to viral-induced type 1 diabetes [Rat] |
| GSE40498 |
Temporal induction of immunoregulatory processes coincides with age-dependent resistance to viral-induced type 1 diabetes |
|
