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Sample GSM1357767 Query DataSets for GSM1357767
Status Public on Mar 28, 2014
Title K-rasG12Dint +HFD+Butyrate, rep2
Sample type RNA
 
Source name duodenum, K-rasG12Dint, HFD + butyrate
Organism Mus musculus
Characteristics strain/background: C57BL/6J mix
genotype/variation: K-rasG12Dint
age: 10 months
Sex: male
tissue: duodenum
treatment: high-fat diet + butyrate
Treatment protocol Mice were euthanized with carbon dioxide inhalation.
Growth protocol Animals were housed at pathogen-free facility, under 12 hours dark/light cycle.
Extracted molecule total RNA
Extraction protocol Tissue samples were homogenized in Trizol buffer and mRNA was isolated in a single-step acid guanidinium thiocyanate-phenol-chloroform extraction following manufacturer's instructions (http://tools.invitrogen.com/content/sfs/manuals/trizol_reagent.pdf). RNA-precipitation was done with ethanol. RNA was diluted in nuclease-free water and concentrations were determined using a Nanodrop spectrophotometer.
Label biotin
Label protocol For each experimental sample, RNA quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100. 0.3 µg of total RNA was used as start Material. The labeling reaction was performed by using the GeneChip® WT PLUS Reagent Kit from Affymetrix (Cat N° 902281) following manufacturer's instructions.
 
Hybridization protocol Biotinylated fragmented ssDNA was hybridized onto the GeneChip® Mouse Gene 1.0 ST Array (Affymetrix) according to the manufacturer's recommendation. The hybridization was performed for 16 h at 45°C in the GeneChip® Hybridization Oven 640 (Affymetrix). Washing and staining of the arrays were done on the GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer's recommendation.
Scan protocol Arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix).
Description group2_2979D
Data processing Data were quantile normalized and log2 transformed using R and Bioconductor package limma.
 
Submission date Mar 26, 2014
Last update date Mar 28, 2014
Contact name Gabriela Salinas
E-mail(s) Gabriela.Salinas-Riester@medizin.uni-goettingen.de
Organization name Universitaetsmedizin Goettingen
Department Department of Human Genetics
Lab NGS Integrative Genomics
Street address Justus-von-Liebig-Weg 11
City Goettingen
State/province Lower-Saxony
ZIP/Postal code 37077
Country Germany
 
Platform ID GPL17777
Series (1)
GSE56257 High-fat diet-mediated dysbiosis promotes intestinal carcinogenesis independent of obesity

Data table header descriptions
ID_REF
VALUE limma normalized signal intensity (log2)

Data table
ID_REF VALUE
100008567_at 7.097316552
100009600_at 6.458042122
100009609_at 3.858034852
100009614_at 6.755246357
100012_at 4.69297268
100017_at 9.171468413
100019_at 8.679253735
100033459_at 4.847860158
100034251_at 8.106795717
100034748_at 6.659536543
100036520_at 7.380037603
100036521_at 8.596008493
100036523_at 7.702498452
100036537_at 5.776010041
100036768_at 6.938854077
100037258_at 11.32288298
100037260_at 7.235483624
100037262_at 7.457979449
100037278_at 8.179594659
100037396_at 6.268968847

Total number of rows: 21187

Table truncated, full table size 442 Kbytes.




Supplementary file Size Download File type/resource
GSM1357767_Muenchen_2979D_knock-out_Tal4_20130723_MoGene-1_0-st-v1.CEL.gz 4.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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