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Sample GSM1347924 Query DataSets for GSM1347924
Status Public on Jul 24, 2014
Title Primary Mouse Hepatocytes exposed to 0.5 % v/v DMSO for 24h, biological rep 2
Sample type RNA
 
Source name primary mouse hepatocytes_0.5 % v/v DMSO for 24h
Organism Mus musculus
Characteristics strain background: C57Bl6
cell type: primary mouse hepatocytes
exposed to: 0.5 % v/v DMSO for 24h
Treatment protocol After the recovery period (40-42 hours), the medium was replaced with fresh medium containing either compound or solvent (0.5% DMSO)
Growth protocol Primary Mouse Hepatocytes were cultured in 6-well plates in a collagen-collagen sandwich and in the presence of serum-free culture medium supplemented with glucagon (7ng/mL), insulin (0.5 U/mL), 2% penicillin/streptomycin and hydrocortison (7.5 µg/mL). The cells were incubated at 37 C and 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated after 24 and 48 hours of incubation with CsA or DMSO in HepG2 total RNA was isolated from cells using miRNeasy mini Kit (Qiagen Westburg bv, Leusden, the Netherlands) according to the manufacturer’s instructions and followed by a DNAse I (Qiagen Inc.) treatment. RNA quantity was measured on a spectrophotometer and quality was determined on a BioAnalyzer (Agilent Technologies, Breda, the Netherlands). Only RNA samples which showed clear 18S and 28S peaks and with a RIN level higher than 8 were used.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA using the 3’ IVT express kit
 
Hybridization protocol 12.5µg of cRNA were hybridized for 16 hr on 45°C on Affymetrix Mouse Genome 430 2.0 Array, using Affymetrix® GeneChip® Fluidics Station 450 and the GeneChip Hybridization, Wash and Stain Kit
Scan protocol Arrays were scanned using Affymetrix GeneArray scanner.
Description DMSO_24h_Exp1_34
Data processing Obtained data sets were re-annotated to the MBNI Custom CDF-files v15.1 (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp) (Dai et al., 2005) and RMA normalized (Irizarry et al., 2003) using the Arrayanalysis.org web service.
The 'complete_data.txt' (of 17,370 data rows) contains ~60 of control probes, which are not included in the sample data table.
 
Submission date Mar 13, 2014
Last update date Jul 24, 2014
Contact name Wim Van den Hof
E-mail(s) vandenhof.wim@gmail.com
Organization name Maastricht University
Department Toxicogenomics
Street address Universiteitssingel 50
City Maastricht
ZIP/Postal code P.O. Box 616, 6200 MD
Country Netherlands
 
Platform ID GPL15967
Series (2)
GSE55881 Expression Profiles of Primary Mouse Hepatocytes treated with Cyclosporin A and solvent control [RNA]
GSE55883 Expression Profiles of Primary Mouse Hepatocytes treated with Cyclosporin A and solvent control

Data table header descriptions
ID_REF
VALUE Log2 of RMA intensity from MBNI custom annotation

Data table
ID_REF VALUE
100008567_at 6.529145112
100009600_at 5.446114309
100012_at 3.273465855
100017_at 8.130523607
100019_at 7.988727956
100034251_at 5.90123391
100034739_at 3.615777626
100034748_at 4.237397564
100036520_at 3.986554614
100036521_at 9.436653091
100036523_at 4.959274427
100036768_at 3.688607948
100037258_at 9.44833508
100037262_at 5.480299709
100037278_at 6.694518505
100038347_at 5.503512093
100038358_at 3.803987375
100038371_at 3.735642686
100038392_at 5.065577119
100038398_at 7.938951311

Total number of rows: 17306

Table truncated, full table size 359 Kbytes.




Supplementary file Size Download File type/resource
GSM1347924_AK5.CEL.gz 3.6 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table
Processed data are available on Series record

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