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Sample GSM984171 Query DataSets for GSM984171
Status Public on Nov 27, 2013
Title JNK1KO BDL 28d rep1
Sample type RNA
 
Source name liver from JNK1 null [JNK1-/-] mice, 28 days after bile duct ligation
Organism Mus musculus
Characteristics treatment: bile duct ligation
time: 28 d
genetic background: C57/BL6
genotype: JNK1 null (JNK1-/-)
gender: male
tissue: liver
age: 12 weeks
Treatment protocol Induction of liver fibrosis was performed in 7-8 weeks old age-matched male mice (n = 9-10 per group) by ligating the common bile duct (BDL). Control treated animals were opened and immediately closed (sham). Mice were sacrificed 48h and 28days later.
Growth protocol JNK1-deficient mice were purchased from Harlan Laboratories (Bar Harbor, ME). JNK1f/f (C57BL/6 background) mice were kindly donated by Dr. Roger J. Davis (Howard Hughes Medical Institute, Chevy Chase, MD) and crossed with transgenic animals expressing the Cre transgene under control of a postnatal activated albumin promoter by crossing giving yield to the JNK1Δhepa strain, mice with specific deletion of JNK1 only in hepatocytes. Mice were maintained on standard laboratory chow.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from the liver using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. 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 (Applied Biosystems, Nieuwekerk a/d IJssel, The Netherlands).
 
Hybridization protocol The Affymetrix GeneChip Mouse Gene 1.1 ST 24-array plate consists of 24 single Gene 1.1 ST peg arrays arranged into the standard 96 well plate format. Array hybridization, washing and scanning were performed on a GeneTitan Instrument according to the manufacturer’s recommendations.
Scan protocol Arrays were scanned on an Affymetrix GeneTitan instrument.
Data processing Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.20.4).
 
Submission date Aug 10, 2012
Last update date Nov 27, 2013
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 (1)
GSE40041 Jnk1 in murine hepatic stellate cells is a crucial mediator of liver fibrogenesis

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

Data table
ID_REF VALUE
10338001 11.09293558
10338002 4.312805839
10338003 9.351396342
10338004 8.683243115
10338005 2.151795064
10338006 2.329735301
10338007 2.479139413
10338008 2.819122097
10338009 6.602717976
10338010 2.161249402
10338011 3.72328429
10338012 2.171962374
10338013 1.979404595
10338014 2.059387547
10338015 2.026399626
10338016 5.297971586
10338017 12.49082992
10338018 4.71533986
10338019 3.439001111
10338020 6.221162112

Total number of rows: 35556

Table truncated, full table size 725 Kbytes.




Supplementary file Size Download File type/resource
GSM984171_G066_C07_25_TW127_232.CEL.gz 4.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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