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| Status |
Public on Oct 01, 2022 |
| Title |
Day40 DRlyp/lyp Rat fed with a normal cereal diet plus Lp299v from age of day21, rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Diabetes prone rats, with homozygous mutation at LYP locus
|
| Organism |
Rattus norvegicus |
| Characteristics |
diet: fed with a normal cereal diet plus Lp299v
strain: DRlyp/lyp strain (diabetes prone)
tissue: pancreatic islets
age: 40 days old
|
| Treatment protocol |
At 21 days of age, DRlyp/lyp rats were weaned onto a normal cereal diet (DRlyp/lyp ND) containing both plant and animal protein sources (LabDiet 5L0D, Purina, St. Louis, MO, USA) or a gluten-free hydrolyzed bovine casein diet (DRlyp/lyp HCD, Modified AIN-93G diet, Dyets Inc., Bethlehem, PA, USA). Subgroups of DRlyp/lyp rats receiving these diets were supplemented with 50 million CFU/gram body weight/day Lp299v (Lactobacillus plantarum 299v; NextFoods, Boulder, CO) by oral gavage from weaning (DRlyp/lyp ND+Lp299v and DRlyp/lyp HCD+Lp299v). Flyp/lyp rats were weaned at 21 days onto ND and did not receive Lp299v (Flyp/lyp ND). Weight and blood glucose (measured with an Ascensia Elite XL glucometer; Bayer, Tarrytown, New York, USA) were measured from 40 day of age; diabetes was defined as blood glucose levels ≥250mg/dl on two consecutive days. Blood was collected by heart puncture from rats under isofluorane anesthesia into EDTA vacutainer tubes (Becton-Dickinson, Franklin Lakes, NJ, USA). Plasma was separated by centrifugation and stored at -80°C. All procedures followed The National Institutes of Health Guide for the Care and Use of Laboratory and were approved by the Medical College of Wisconsin Institutional Animal Care and Use Committee (Assurance Number A3102-01).
|
| Growth protocol |
DRlyp/lyp and Flyp/lyp rats were maintained at The Medical College of Wisconsin (MCW) under specific pathogen-free conditions with standard light/dark cycles. Rats were provided chow and water ad libitum. All federal guidelines for use and care of laboratory animals (http://grants1.nih.gov/grants/olaw/references/phspol.htm) were followed.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted Trizol (Invitrogen, Carlsbad, CA, USA). RNA was amplified/labeled using Affymetrix 3' IVT Express 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.
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| |
|
| Hybridization protocol |
The Affymetrix GeneChip rat genome RG230 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 interrogating 31099 transcripts
|
| Data processing |
Array images were quantified with Affymetrix Expression Console Software and normalized with Robust Multichip Analysis (Bioconductor - www.bioconductor.org) to determine signal log ratios [26]. Gene expression differences were also evaluated by principle component analyses, and the statistical significance of differential gene expression and false discovery rates (FDR) were derived through RankProduct (RP) statistic from Bioconductor.
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| |
|
| Submission date |
Mar 14, 2022 |
| Last update date |
Oct 02, 2022 |
| 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 |
GPL1355 |
| Series (1) |
| GSE198617 |
Probiotic supplementation with Lactiplantibacillus plantarum 299v modulates ER and oxidative stress pathways in ?-cells and prevents Type 1 diabetes in gluten-free BioBreeding Rats |
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