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Sample GSM7056349 Query DataSets for GSM7056349
Status Public on Aug 25, 2023
Title BXD73a_CD
Sample type RNA
 
Source name proximal colon, chow diet
Organism Mus musculus
Characteristics strain: BXD73a
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 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 BXD73a mice fed on chow 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 11.08153
TC0100000018.mm.2 5.25275
TC0100000021.mm.2 9.71786
TC0100000022.mm.2 4.22982
TC0100000023.mm.2 6.54675
TC0100000027.mm.2 11.07534
TC0100000039.mm.2 7.43352
TC0100000041.mm.2 6.30479
TC0100000044.mm.2 7.40251
TC0100000045.mm.2 6.88449
TC0100000048.mm.2 9.66806
TC0100000055.mm.2 6.7299
TC0100000056.mm.2 7.80924
TC0100000064.mm.2 7.91744
TC0100000071.mm.2 5.72598
TC0100000082.mm.2 6.30991
TC0100000092.mm.2 11.2981
TC0100000097.mm.2 8.22689
TC0100000101.mm.2 5.23858
TC0100000103.mm.2 8.81943

Total number of rows: 21951

Table truncated, full table size 559 Kbytes.




Supplementary file Size Download File type/resource
GSM7056349_BXD73a_CD.CEL.gz 1.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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