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Sample GSM1975507 Query DataSets for GSM1975507
Status Public on Jan 27, 2016
Title Liver_mouse_FXRKO_INT747_rep6
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: 44
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_H9_LIVER_44_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 10.78273988
10338002 3.796872685
10338003 8.837253983
10338004 7.927412869
10338005 1.632423402
10338006 1.923664512
10338007 2.067552299
10338008 2.367808588
10338009 5.480047231
10338010 1.684293787
10338011 3.296484941
10338012 1.798469392
10338013 1.454929022
10338014 1.554344309
10338015 1.488671747
10338016 4.611984928
10338017 12.03236638
10338018 4.116645794
10338019 3.049827308
10338020 5.388354765

Total number of rows: 35556

Table truncated, full table size 725 Kbytes.




Supplementary file Size Download File type/resource
GSM1975507_A410_H9_LIVER_44_FXRKO_INT747_2.CEL.gz 4.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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