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Sample GSM4171614 Query DataSets for GSM4171614
Status Public on Jun 08, 2020
Title Liver, control mouse, replicate 3
Sample type RNA
 
Source name Liver, control mouse, aged 52 weeks
Organism Mus musculus
Characteristics genotype/variation: Control
tissue: Liver
treatment: None
age: 52 weeks
mouseid: TW187-150
Treatment protocol Mice had free access to chow and water. Depending on the mouse model and experiment, livers were removed from mice at the age of 8 or 52 weeks, or at the indicated time points after treatment with diethylnitrosamine (DEN) or after bile duct ligation (BDL). After removal, tissues were immediately snap-frozen in liquid nitrogen and stored at -80 until RNA isolation.
Growth protocol Alb-Cre and Jnk2-deficient mice on a C57BL/6 background were purchased from The Jackson Laboratory (Bar Harbor, ME). Jnk1LoxP/LoxP /Jnk2−/− (JNKΔhepa) mice were created as previously reported (Cubero et al., 2016; Das et al., 2007; Das et al., 2009). NEMO∆hepa/JNKΔhepa mice, and their respective controls (NEMO∆hepa and NEMOf/f mice) were created as described in the current manuscript.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated by Directzol RNA Miniprep (Zymo Research, Irvine, CA). 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 analysis 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 Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).
 
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 (Affymetrix, Santa Clara, CA, USA).
Scan protocol Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).
Data processing Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.50.0).
 
Submission date Nov 15, 2019
Last update date Jun 08, 2020
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)
GSE140498 Hepatocytic c-Jun N-terminal kinases (JNK)-1/2 function determines cell fate during carcinogenesis

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

Data table
ID_REF VALUE
10338001 11.31067196
10338002 4.119409354
10338003 9.495426791
10338004 8.7589442
10338005 1.667893513
10338006 1.934075671
10338007 2.095979293
10338008 2.410019245
10338009 6.050367764
10338010 1.70184157
10338011 3.589952414
10338012 1.810587492
10338013 1.505382243
10338014 1.591624833
10338015 1.545969716
10338016 5.061802951
10338017 12.36335856
10338018 4.466986898
10338019 3.183939094
10338020 5.865822484

Total number of rows: 35556

Table truncated, full table size 725 Kbytes.




Supplementary file Size Download File type/resource
GSM4171614_G197_A09_03_TW187_150.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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