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Sample GSM1975498 Query DataSets for GSM1975498
Status Public on Jan 27, 2016
Title Liver_mouse_FXRKO_INT747_rep3
Sample type RNA
 
Source name liver, FXR knockout, FXR agonist OCA (INT-747) for 7 days
Organism Mus musculus
Characteristics strain/background: C57BL/6
genotype/variation: FXR KO
gender: male
tissue: liver
treatment: OCA (INT-747) (10 mg/kg/day, dissolved in 1% methyl cellulose
time point: 7 days
mouse_id: 41
Treatment protocol At the age of 9-12 weeks, mice received a daily oral gavage with the semi-synthetic FXR agonist obeticholic acid (OCA, INT-747, 6α-ethyl-chenodeoxycholic acid; 10 mg/kg/day), or vehicle (1% methyl cellulose) for 7 days. Livers were then isolated, snap frozen in liquid nitrogen, and stored at -80°C.
Growth protocol Male C57BL/6 wild-type (WT) and FXR-/- mice [PMID: 11030617] were housed in a room with controlled temperature (20-24°C), relative humidity (55%±15%) and a 12h light dark cycle. Mice were fed chow and demineralized water ad libitum.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using RNeasy micro kit from Qiagen. 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).
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 according to the manufacturer's recommendations.
Scan protocol Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.
Description A410_E9_LIVER_41_FXRKO_INT747_2.CEL
Liver tissue from FXR knockout mouse treated with the FXR agonist OCA (INT-747) (10 mg/kg/day, dissolved in 1% methyl cellulose) by oral gavage for 7 days.
Data processing Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.34.0).
 
Submission date Dec 18, 2015
Last update date Jan 27, 2016
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 (2)
GSE76162 Gene expression profiling in human precision-cut liver slices upon treatment with the FXR agonist obeticholic acid [mouse]
GSE76163 Gene expression profiling in human precision-cut liver slices upon treatment with the FXR agonist obeticholic acid

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

Data table
ID_REF VALUE
10338001 10.78188312
10338002 3.91885593
10338003 8.865334408
10338004 7.995515023
10338005 1.705427637
10338006 1.938095493
10338007 2.060691702
10338008 2.382953894
10338009 5.814213274
10338010 1.732904603
10338011 3.364441455
10338012 1.844493327
10338013 1.488103419
10338014 1.594415155
10338015 1.542403666
10338016 4.870223222
10338017 12.00172582
10338018 4.298234362
10338019 3.074240089
10338020 5.747448135

Total number of rows: 35556

Table truncated, full table size 725 Kbytes.




Supplementary file Size Download File type/resource
GSM1975498_A410_E9_LIVER_41_FXRKO_INT747_2.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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