strain: BXD85 age: 29 weeks gender: Male tissue: Proximal colon diet_id: CD diet_description: chow diet dietary_intervention: Mice were fed a chow diet (CD) ad libitum through their entire life. diet_composition: fat: 6% kCal, protein: 20% kCal, carbohydrates: 74% kCal diet_ref: Harlan, 2018, Indianapolis, IN, USA
Treatment protocol
Mice were fed CD ad libitum until 8 weeks of age. From 8 weeks to 29 weeks, half of the cohort was fed ad libitum HFD and the rest continued to be fed a CD (Fig.1 A). CD composition: 6% kCal fat, 20% kCal protein and 74% kCal of carbohydrates (Harlan, 2018, Indianapolis, IN, USA). HFD composition: 60% kCal fat, 20% kCal protein and 20% kCal of carbohydrates (Harlan, 06414, Indianapolis, IN, USA).
Growth protocol
In groups of 3-5 animals from same strain and under same diet, in isolator cages with individual air filtration (500 cm2, GM500, Tecniplast) and provided water ad libitum
Extracted molecule
total RNA
Extraction protocol
A ~1 cm portion of the proximal half part of the colon was excised following euthanasia and immediately stored in liquid nitrogen. Total RNA was extracted using trizol. RNA concentration was assessed using a Nanodrop and RNA integrity was assessed using a Bioanalyzer. RNA extracts from approximately 5 animals of the same strain fed the same diet, were pooled at equal mass concentration and cleaned up using the Qiagen RNEasy kit.
Label
biotin
Label protocol
100ng of total RNA was amplified using the Ambion® WT Expression Kit from life technologies (part number 4411974) and 5,500ng of cDNA was fragmented and labeled using the Affymetrix WT terminal labeling kit (part number 900671) all following manufacturers protocols
Hybridization protocol
Labeled cDNA was hybridized on an Affymetrix Clariom S Assay microarray platform (GPL23038) in ~16 hours of incubation, then washed and stained using an Affymetrix 450 Fluidics Station according to Affymetrix protocols.
Scan protocol
Arrays were scanned on Affymetrix GSC3000 7G Scanner.
Description
Gene expression data from pooled RNA extract of proximal colon samples collected on 29 weeks old male BXD85 mice fed on chow diet
