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Sample GSM1119725 Query DataSets for GSM1119725
Status Public on Oct 21, 2013
Title Liver_pool_acetate_infusion
Sample type RNA
 
Source name liver, pooled RNA of 6 mice, 6 hrs after infusion with 0.3 M sodium [1-13C]acetate
Organism Mus musculus
Characteristics strain: C57Bl/6J
gender: male
age: 16-17 weeks
tissue: liver
treatment: infused with 0.3 M sodium [1-13C]acetate
Treatment protocol Mice were equipped with a permanent cecum catheter and allowed a recovery period of at least 5 days. Cecal cannulas were flushed daily with phosphate buffered saline. On the day of the experiment, mice were individually housed and fasted from 6:00 to 10:00 a.m. All infusion experiments were performed in conscious, unrestrained mice. Four different groups received either a control phosphate-buffered saline solution, a 0.3 M sodium [1-13C]acetate (99 atom %, Sigma-Aldrich) solution, a 0.3 M sodium [2-13C]propionate (99 atom %, Sigma-Aldrich) solution or a 0.3 M sodium [2,4-13C2]butyrate (99 atom %, Sigma-Aldrich) solution infused via the cecum catheter at an infusion rate of 0.2 ml/h. The resulting rate of infusion of labeled SCFA was 2.4 mmol/h/kg. After 6 h of infusion, animals were killed by cardiac puncture under isoflurane anesthesia. Livers were removed, freeze-clamped, and stored at -80 °C for RNA isolation.
Growth protocol Male C57Bl/6J mice (Charles River, L’Arbresle Cedex, France), 2 months of age, were housed in a light- and temperature-controlled facility (lights on 6:30 a.m. to 6:30 p.m., 21 °C). Mice were fed a semi-synthetic diet based on Research Diets’ formulations D12450B, with adaptations regarding type of fat (palm oil instead of lard) and carbohydrates, for 6 weeks and had free access to drinking water.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from livers using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0). For array analysis, RNA of 4-8 mice per group was subsequently pooled at a concentration of 500 ng/mouse.
Label biotin
Label protocol One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).
 
Hybridization protocol Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.
Scan protocol Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).
Data processing Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.22.0).
 
Submission date Apr 09, 2013
Last update date Oct 21, 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)
GSE45926 Gut-derived short-chain fatty acids are vividly assimilated into host carbohydrates and lipids

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

Data table
ID_REF VALUE
10338001 11.25704735
10338002 4.480040144
10338003 9.247499441
10338004 6.38212927
10338005 2.045140608
10338006 2.280450169
10338007 2.502092133
10338008 2.782178932
10338009 6.491892655
10338010 2.065427564
10338011 3.73134665
10338012 2.185057286
10338013 1.894743597
10338014 1.961840469
10338015 1.880510238
10338016 5.415237168
10338017 12.35716058
10338018 4.836119148
10338019 3.523918252
10338020 6.272580025

Total number of rows: 35556

Table truncated, full table size 725 Kbytes.




Supplementary file Size Download File type/resource
GSM1119725_G050_H10_L_P14_ACETATE.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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