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Sample GSM1484948 Query DataSets for GSM1484948
Status Public on Aug 24, 2014
Title group5, control CAR/PXR h 5029
Sample type RNA
 
Source name mouse liver
Organism Mus musculus
Characteristics tissue: liver
genotype: human CAR/PXR
age: 9 to 11 weeks
treatment: control
time point: 119 days
donorid: 5029
Treatment protocol Phenobarbital (PB; free acid, >99.0%, Sigma, St Louis, MO, no. 04710, 0.05% (wt/vol) in drinking water) was administered to one group through ad libitum access to drinking water, as previously reported (see methods in PMID: 24690595). Mice were reated with PB starting at 8 weeks of age. PB was adminis- tered via the drinking water (PB solution prepared freshly every fourth day) at concentrations of 0.005, 0.01, 0.02, and 0.05% (wt/vol). Mice were kept on a 12 h dark/light cycle and had ac- cessed to food and water ad libitum. All animals were sacrificed between 9 and 11 a.m. to avoid circadian influences.checked daily for activity and behavior and sacrificed on the indicated dates. Liver (incl. left, caudal and median parts) were sampled. To ensure sample homo- geneity for different molecular profiling methods, frozen liver samples were reduced to powder with CovarisCryoprep (Co- varis Inc., Woburn, MA) system and aliquoted on dry ice. For the 4-week dose response study, mice (n = 4 per group) were treated with PB starting at 8 weeks of age. PB was adminis- tered via the drinking water (PB solution prepared freshly every fourth day) at concentrations of 0.005, 0.01, 0.02, and 0.05% (wt/vol). Mice were kept on a 12 h dark/light cycle and had ac- cessed to food and water ad libitum. All animals were sacrificed between 9 and 11 a.m. to avoid circadian influences.
Growth protocol C57BL/6 male wild-type, knock-out CARKO -PXRKO and humanized CARh - PXRh mice were obtained from TaconicArtemis (Germany). For the 13-week time course study, 9–11 week-old mice (age selected to avoid the confounding effect of liver maturation observed in younger animals) were allowed to acclimatize for 5 days prior to being randomly divided into two treatment groups (n = 5 per time point).
Extracted molecule total RNA
Extraction protocol Frozen liver samples were homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and subsequently purified on a silica-gel-based-membrane (RNeasy, Qiagen, Venlo, Netherlands) according to the manufacturer’s instruc- tions. RNA quality was assessed by measuring the RIN (RNA Integrity Number) using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). RNA was stored at −80◦C. miRNA was quantified using the Rediplate Ribogreen RNA quantitation kit (Life Technologies).
Label biotin
Label protocol Processing of GeneChip experiments was conducted as recommended by the manufacturer of the GeneChip system (Affymetrix, Santa Clara, CA).
 
Hybridization protocol Processing of GeneChip experiments was conducted as recommended by the manufacturer of the GeneChip system (Affymetrix, Santa Clara, CA).
Scan protocol Processing of GeneChip experiments was conducted as recommended by the manufacturer of the GeneChip system (Affymetrix, Santa Clara, CA).
Description group5, control CAR/PXR h
NUID-0000-0136-0289
Data processing Affymetrix CEL files were normalized using the Robust Multichip Average (RMA) from R/Bioconductor (reported expressino values are log base 2 transformed). Quality metrics from arrays prior and after normalization using Bioconductor’s array QualityMetrics package (Kauffmann et al., 2009) were within acceptable limits except for 11 chips which were removed from subsequent analyses (not included).
 
Submission date Aug 22, 2014
Last update date Jun 08, 2015
Contact name Jonathan Moggs
E-mail(s) jonathan.moggs@novartis.com
Organization name Novartis
Street address Fabrikstrasse 2
City Basel
ZIP/Postal code 4056
Country Switzerland
 
Platform ID GPL1261
Series (3)
GSE60684 Phenobarbital Induces Cell Cycle Transcriptional Responses in Mouse Liver Humanized for Constitutive Androstane and Pregnane X Receptors (mRNA)
GSE60693 Phenobarbital Induces Cell Cycle Transcriptional Responses in Mouse Liver Humanized for Constitutive Androstane and Pregnane X Receptors
GSE68387 IMI MARCAR Project: towards novel biomarkers for cancer risk assessment

Data table header descriptions
ID_REF
VALUE RMA

Data table
ID_REF VALUE
1415670_at 8.48809121
1415671_at 10.00232072
1415672_at 10.65791856
1415673_at 7.026640871
1415674_a_at 8.522045249
1415675_at 7.295211283
1415676_a_at 10.66677774
1415677_at 9.921000023
1415678_at 10.03773104
1415679_at 10.45429569
1415680_at 8.205919155
1415681_at 9.265706109
1415682_at 7.642404007
1415683_at 10.50041793
1415684_at 9.483938032
1415685_at 9.555112203
1415686_at 9.636500398
1415687_a_at 10.85306423
1415688_at 10.31368347
1415689_s_at 8.848792081

Total number of rows: 45101

Table truncated, full table size 1026 Kbytes.




Supplementary file Size Download File type/resource
GSM1484948_NUID-0000-0136-0289.cel.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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