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Sample GSM805243 Query DataSets for GSM805243
Status Public on Sep 15, 2013
Title jejunum_WT_repl2
Sample type RNA
 
Source name jejunum from wild type mouse (C57BL/6), maintained on chow, 2hrs after lipid load, replicate 2
Organism Mus musculus
Characteristics strain: C57BL/6
genotype/variation: wild type
gender: male
tissue: jejunum
age: 14-16 wks
sample type: scraped off epithelial cells, 2hrs after oral lipid load
Treatment protocol Animals were maintained on regular lab chow. Mice were used at age between 14-16 weeks. For sampling of liver tissue, mice were fasted over night (16hrs). For sampling of small intestine, overnight fasted mice first received an intragastric load of 200 µL olive oil (Carbonell, Cordoba, Spain), and 2 hrs later small intestines were removed. The small intestine was subsequently divided into duodenum, jejunum, and ileum, and the epithelial cell layer was scraped off. All tissue samples were immediately snap-frozen in liquid nitrogen and stored at -80°C for RNA isolation.
Growth protocol Caspase-1 null mice were backcrossed ten generations to C57Bl/6 mice and age-matched wild-type C57Bl/6J mice were used as control mice. Mice were housed under standard conditions with a 12-hour light-dark cycle and were fed a standard mouse chow diet with free access to water. Experiments were performed in 14 to 16-week old animals.
Extracted molecule total RNA
Extraction protocol Total RNA was obtained by extraction with TRIzol reagent (Invitrogen, Carlsbad, CA), followed by DNAse treatment and column purification using the RNeasy mini kit (Qiagen, Hilden, Germany). RNA integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands) with 6000 Nano Chips. RNA was judged as suitable only if samples showed intact bands of 18S and 28S ribosomal RNA subunits, displayed no chromosomal peaks or RNA degradation products, and had a RNA integrity number (RIN) above 8.0.
Label biotin
Label protocol The Ambion WT Expression kit (Life Technologies, Carlsbad, CA; P/N 4411974) in conjunction with the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix, Santa Clara, CA; P/N 900671) was used for the preparation of labeled cDNA from 100ng of total RNA without rRNA reduction.
 
Hybridization protocol The Affymetrix GeneChip Mouse Gene 1.1 ST arrays are peg arrays arranged into the standard 96 well plate format. The 24 arrays that were used in this experiment were provided as 1x24 array plate. Array hybridization, washing and scanning were performed on a GeneTitan Instrument according to the manufacturer’s recommendations.
Scan protocol Arrays were scanned on an Affymetrix GeneTitan instrument.
Data processing Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.16.0). The SI samples were normalzed together, separately from the liver samples.
 
Submission date Sep 30, 2011
Last update date Sep 15, 2013
Contact name Guido Hooiveld
E-mail(s) guido.hooiveld@wur.nl
Organization name Wageningen University
Department Div. Human Nutrition & Health
Lab Nutrition, Metabolism & Genomics Group
Street address HELIX, Stippeneng 4
City Wageningen
ZIP/Postal code NL-6708WE
Country Netherlands
 
Platform ID GPL11533
Series (1)
GSE32515 Caspase-1 deficiency reduces intestinal and hepatic triglyceride-rich lipoprotein secretion

Data table header descriptions
ID_REF
VALUE RMA signal (as log2)

Data table
ID_REF VALUE
10338001 11.3114204
10338002 4.636918715
10338003 9.429617137
10338004 8.590041384
10338005 2.223026376
10338006 2.432036781
10338007 2.713188231
10338008 3.160288104
10338009 6.839819069
10338010 2.230583839
10338011 4.204512286
10338012 2.324545694
10338013 1.984785039
10338014 2.10622402
10338015 2.014143096
10338016 5.665014633
10338017 12.12655599
10338018 5.072508303
10338019 3.670332432
10338020 6.490234366

Total number of rows: 35556

Table truncated, full table size 725 Kbytes.




Supplementary file Size Download File type/resource
GSM805243.CEL.gz 4.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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