|
| Status |
Public on Sep 01, 2012 |
| Title |
UPN727 cells, recent onset 2109 plasma |
| Sample type |
RNA |
| |
|
| Source name |
UPN727 cells stimulated with RO2109 plasma
|
| Organism |
Homo sapiens |
| Characteristics |
protocol: stimulated with RO2109 plasma
responder cell line: UPN727
|
| Treatment protocol |
Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% of autologous, longitudinal, longstanding (LS), healthy control (HC), or recent onset (RO) T1D 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 (9 hours optimal for cryopreserved PBMCs) total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).
|
| Growth protocol |
Commercial cryopreserved PBMCs of healthy Caucasian male donor UPN727 were thawed and washed per the manufacturer’s protocol (Cellular Technology Ltd., Shaker Heights, OH).
|
| 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 GeneChip human genome U133 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 |
Gene expression data from UPN727 cells stimulated with recent onset (RO) Type 1 Diabetic plasma
|
| Data processing |
Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log ratios. Each sample was independently analyzed. The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Paired 2 sample ttest as a statistic analysis method in Partek GS.
|
| |
|
| Submission date |
Feb 10, 2012 |
| Last update date |
Sep 01, 2012 |
| Contact name |
Martin Hessner |
| E-mail(s) |
[email protected]
|
| 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 |
GPL570 |
| Series (2) |
| GSE35713 |
Transcriptional Signatures as a Disease-Specific and Predictive Inflammatory Biomarker for Type 1 Diabetes |
| GSE35725 |
Transcriptional Signatures as a Disease-Specific and Predictive Inflammatory Biomarker for Type 1 Diabetes [T1D_114] |
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