|
| Status |
Public on Oct 01, 2015 |
| Title |
UPN727 cells, Crohn’s disease (CD) plasma patients 03 |
| Sample type |
RNA |
| |
|
| Source name |
UPN727 cells stimulated with CD03 Plasma
|
| Organism |
Homo sapiens |
| Characteristics |
responder cell line: UPN727
diagnosis of plasma donor: Crohn’s disease (CD)
|
| Treatment protocol |
Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% of Crohn’s disease (CD), ulcerative colitis (UC), and unrelated healthy control (uHC) plasma cultured. 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 express 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 Crohn’s disease (CD) plasma
|
| Data processing |
Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensity/ratios. The statistical significance of differential gene expression and false discovery rates (FDR) were derived through ANOVA function in Partek GS.
|
| |
|
| Submission date |
Aug 04, 2015 |
| Last update date |
Oct 01, 2015 |
| 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 |
GPL570 |
| Series (1) |
| GSE71730 |
Plasma induced signatures reveal an extracellular milieu possessing an immunoregulatory bias in treatment naïve inflammatory bowel disease |
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