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Sample GSM833949 Query DataSets for GSM833949
Status Public on Apr 01, 2013
Title AK12_PMH_48hr_10µM_Csa_1
Sample type RNA
 
Source name PMH_48hour_10µM_cyclosporin A
Organism Mus musculus
Characteristics strain: C57Bl6
gender: male
cell type: primary hepatocytes
Treatment protocol The primairy mouse hepatocytes were exposed as to 10 μM cyclosporine A or 0.5 % DMSO as a vehicle control for 48 hours.
Growth protocol Cells from three independent biological replicates with viability > 80 were used and cultured on collagen gel-precoated six-well plates at a density of 6.5 105 cells/ml. Cells were allowed to attach for 2 to 4 h at 37°C in a humidified chamber with 95:5% air/CO2 in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal calf serum, 0.5 U/ml insulin, 7 ng/ml glucagon, and 2% penicillin/streptomycin (5000 U/ml penicillin; 5000 μm/ml streptomycin). After attachment, medium containing unattached cells and debris was removed by washing, and the cultures were overlaid with a second collagen layer to form a collagen-collagen sandwich culture. Primary cultures of mouse hepatocytes were cultured at 37°C in a humidified chamber with 95:5% air/CO2 in serum-free culture medium supplemented with 0.5 U/ml insulin, 7 ng/ml glucagon, 7.5 μg/ml hydrocortisone, and 2% penicillin/streptomycin (5000 U/ml penicillin; 5000 μm/ml streptomycin). Cells from three independent biological experiments (each from a different animal) were harvested at 48 h after isolation for gene expression analysis.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated after 48 hours of incubation with cyclosporin A or DMSO. 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 cRNA targets were prepared according to the Affymetrix protocol.
 
Hybridization protocol The targets were hybridized according to the manufacturer's recommended procedures on high-density oligonucleotide GeneChips (Affymetrix Mouse Genome 430 2.0 GeneChip arrays).
Scan protocol The GeneChips were washed and stained using a fluidics station by Affymetrix and scanned in an Affymetrix GeneArray scanner.
Description SAMPLE 4
Gene expression data from Primary mouse hepatocytes exposed to 10µM Cyclosporin A or 0.5 % DMSO
Data processing First, the quality of all arrays was inspected using arrayQC, an in-house quality control pipeline that generates virtual images, boxplots, correlation plots, clustering images, MvA and PCA plots. Spike-ins were used for all arrays as an extra quality check. Within this dataset, no arrays were technically deviating. The CustomCDF annotation (Affymetrix mouse4302) (Version 11.0.1, ENTREZG) from BrainArray Microarray were used. The Affymetrix .CEL files were imported in R 2.11.0 using the affy library in BioConductor. All probes were reannotated using the BrainArray customCDF files (EntrezGene, version 11.0.1), followed by a RMA normalization step. Prior to the statistical analysis all probesets (excluding positive and negative controls spotted in the array) had to pass a detection filter criteria [Present/Marginal >= 2 out of 3 biological replicates per condition, control or treated with CsA], resulting in a total of 10,848 reporters.
 
Submission date Nov 16, 2011
Last update date Apr 01, 2013
Contact name Anke Van Summeren
Organization name Maastricht University
Department Toxicogenomics
Street address Universiteitssingel 50
City Maastricht
ZIP/Postal code P.O. Box 616
Country Netherlands
 
Platform ID GPL14661
Series (1)
GSE33742 Drug-induced hepatotoxicity screening in primary mouse hepatocytes, an Omics approach.

Data table header descriptions
ID_REF
VALUE RMA normalized signal intensity

Data table
ID_REF VALUE
15945_at 9.641328036
56312_at 13.50805496
58185_at 10.17693708
241520_at 10.57736682
19250_at 10.6009485
83924_at 8.334056744
235973_at 6.95145894
17988_at 11.93605097
219065_at 8.177182265
16854_at 13.56792681
12994_at 9.455137883
78248_at 8.162001609
67434_at 9.898986562
620695_at 11.96664137
224079_at 9.442059962
58207_at 9.868572725
29858_at 12.35621758
230157_at 8.225753494
12514_at 11.61374227
53626_at 5.741432714

Total number of rows: 16331

Table truncated, full table size 338 Kbytes.




Supplementary file Size Download File type/resource
GSM833949_AK12.CEL.gz 3.7 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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