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Sample GSM1975488 Query DataSets for GSM1975488
Status Public on Jan 27, 2016
Title Liver_mouse_WT_vehicle_rep2
Sample type RNA
 
Source name liver, wild-type, vehicle for 7 days
Organism Mus musculus
Characteristics strain/background: C57BL/6
genotype/variation: wild type
gender: male
tissue: liver
treatment: vehicle (1% methyl cellulose)
time point: 7 days
mouse_id: 10
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_B7_LIVER_10_WT_VEHICLE.CEL
Liver tissue from wild-type 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 11.18370462
10338002 4.147909577
10338003 9.412414865
10338004 8.523082889
10338005 1.77694638
10338006 1.93363014
10338007 2.075057017
10338008 2.392485636
10338009 5.976213546
10338010 1.738493188
10338011 3.44994509
10338012 1.893299318
10338013 1.572679073
10338014 1.654223135
10338015 1.592074037
10338016 4.883148469
10338017 12.30564776
10338018 4.404032935
10338019 3.179740406
10338020 5.754662408

Total number of rows: 35556

Table truncated, full table size 725 Kbytes.




Supplementary file Size Download File type/resource
GSM1975488_A410_B7_LIVER_10_WT_VEHICLE.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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