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Sample GSM7056391 Query DataSets for GSM7056391
Status Public on Aug 25, 2023
Title BXD67_HFD
Sample type RNA
 
Source name proximal colon, chow diet
Organism Mus musculus
Characteristics strain: BXD67
age: 29 weeks
gender: Male
tissue: Proximal colon
diet_id: HFD
diet_description: high fat diet
dietary_intervention: Mice were fed a chow diet (CD) ad libitum until 8 weeks of age. From 8 weeks until heuthanasia, mice were then fed a high-fat diet (HFD) ad libitum.
diet_composition: fat: 60% kCal, protein: 20% kCal
diet_ref: Harlan, 06414, 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 AmbionĀ® 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 BXD67 mice fed on high fat diet
Data processing Intensities were processed using the apt-probeset-summarize script from the Array Power Tool suite (version 2.11.3, https://downloads.thermofisher.com/APT/APT_2.11.3/apt_2.11.3_linux_64_bit_x86_binaries.zip) with the gc-sst-rma-sketch standard method. Data processing code deposited at https://doi.org/10.5281/zenodo.4899683.
 
Submission date Feb 22, 2023
Last update date Aug 25, 2023
Contact name Xiaoxu Li
E-mail(s) xiaoxu.li@epfl.ch
Organization name EPFL
Street address Station 15 - CH
City Lausanne
ZIP/Postal code 1015
Country Switzerland
 
Platform ID GPL23038
Series (1)
GSE225791 Genetic and dietary modulators of inflammation in the gastro-intestinal tract of BXD genetic reference population

Data table header descriptions
ID_REF
VALUE GC-correction, scale-intensities, RMA background adjustment, quantile-normalization, median polish (log2)

Data table
ID_REF VALUE
TC0100000014.mm.2 10.23107
TC0100000018.mm.2 5.26354
TC0100000021.mm.2 9.33411
TC0100000022.mm.2 5.0844
TC0100000023.mm.2 6.58128
TC0100000027.mm.2 11.20364
TC0100000039.mm.2 7.63254
TC0100000041.mm.2 6.51772
TC0100000044.mm.2 7.29514
TC0100000045.mm.2 6.53105
TC0100000048.mm.2 10.30873
TC0100000055.mm.2 6.74054
TC0100000056.mm.2 6.68874
TC0100000064.mm.2 7.19195
TC0100000071.mm.2 4.39037
TC0100000082.mm.2 5.4231
TC0100000092.mm.2 10.81333
TC0100000097.mm.2 7.50255
TC0100000101.mm.2 5.39579
TC0100000103.mm.2 9.81112

Total number of rows: 21951

Table truncated, full table size 559 Kbytes.




Supplementary file Size Download File type/resource
GSM7056391_BXD67_HFD.CEL.gz 1.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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