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Sample GSM4171635 Query DataSets for GSM4171635
Status Public on Jun 08, 2020
Title Liver, NEMO/JNK1Δhepa double knockout mouse, replicate 3
Sample type RNA
 
Source name Liver, NEMO/JNK1Δhepa double knockout mouse aged 8 weeks
Organism Mus musculus
Characteristics genotype/variation: NEMO/JNK1<delta>hepa double knockout
tissue: Liver
treatment: None
age: 8 weeks
mouseid: TW187-735
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).
Description NEMO/JNK1Δhepa double knockout
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 10.95746574
10338002 3.852975087
10338003 8.983762616
10338004 8.014764627
10338005 1.612997536
10338006 1.863447253
10338007 1.962043287
10338008 2.32847899
10338009 5.517937563
10338010 1.657133699
10338011 3.320005982
10338012 1.75905616
10338013 1.487993698
10338014 1.578760661
10338015 1.556598259
10338016 4.62058362
10338017 12.14213576
10338018 4.131466457
10338019 3.011044054
10338020 5.431578228

Total number of rows: 35556

Table truncated, full table size 725 Kbytes.




Supplementary file Size Download File type/resource
GSM4171635_G197_H09_24_TW187_735.CEL.gz 4.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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