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Sample GSM1975486 Query DataSets for GSM1975486
Status Public on Jan 27, 2016
Title Liver_mouse_FXRKO_vehicle_rep1
Sample type RNA
 
Source name liver, FXR knockout, vehicle for 7 days
Organism Mus musculus
Characteristics strain/background: C57BL/6
genotype/variation: FXR KO
gender: male
tissue: liver
treatment: vehicle (1% methyl cellulose)
time point: 7 days
mouse_id: 35
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_A9_LIVER_35_FXRKO_VEHICLE.CEL
Liver tissue from FXR knockout mouse treated with vehicle (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 10.93078138
10338002 4.021174613
10338003 9.119161708
10338004 8.204185198
10338005 1.627767011
10338006 1.822405577
10338007 1.962422907
10338008 2.332160414
10338009 5.710127321
10338010 1.660135541
10338011 3.353974796
10338012 1.733701563
10338013 1.427785998
10338014 1.50966391
10338015 1.444041151
10338016 4.86454495
10338017 12.02610219
10338018 4.295068336
10338019 3.060410704
10338020 5.641242304

Total number of rows: 35556

Table truncated, full table size 725 Kbytes.




Supplementary file Size Download File type/resource
GSM1975486_A410_A9_LIVER_35_FXRKO_VEHICLE.CEL.gz 4.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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