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Sample GSM935108 Query DataSets for GSM935108
Status Public on Dec 05, 2013
Title PMH exposed to PBS for 24h, biological rep 2
Sample type RNA
 
Source name primary hepatocytes
Organism Mus musculus
Characteristics cell line: PMH
treatment: PBS, 0.5%
time: 24h
Treatment protocol After a recovery period of 40-42h, the Dulbecco's Modified Eagle's culture medium was replaced by culture medium containing cisplatin or a vehicle control (0.5% of PBS).
Growth protocol Primary mouse hepatocytes were isolated from adult male C57BL/6 mice using a perfusion method and cultured between a collagen-collagen sandwich formation in two six wells plates
Extracted molecule total RNA
Extraction protocol Qiazol extraction was performed using the miRNAeasy kit from Qiagen according to the manufacturer’s protocol
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 GeneChip 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 genechip scanner 3000 7G
Description PBS_24h_Ex2
Data processing Obtained data sets were re-annotated to the MBNI Custom CDF-files (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 NuGOExpressionFileCreator, an enhanced version of the standard ExpressionFileCreator module that is present in GenePattern (De Groot et al., 2008). The resulting 16,395 probe sets represent 16,331 unique genes and 64 internal controls
 
Submission date May 22, 2012
Last update date Dec 05, 2013
Contact name Linda Rieswijk
E-mail(s) linda.rieswijk@maastrichtuniversity.nl
Organization name Maastricht University
Department Toxicogenomics
Street address Universiteitssingel 50
City Maastricht
ZIP/Postal code 6229 ER
Country Netherlands
 
Platform ID GPL15592
Series (2)
GSE38123 Expression Profiles of PMH treated with 7µM of the genotoxic compound cisplatin
GSE38124 Characterization of cisplatin-induced transcriptomics responses in primary mouse hepatocytes, HepG2 cells and mouse embryonic stem cells shows a strong conservation of involved transcription factors

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

Data table
ID_REF VALUE
11287 13.44394593
11298 7.128604074
11302 6.21926955
11303 7.928228902
11304 4.870394749
11305 6.838877614
11307 5.203823963
11308 9.232706617
11350 6.55549421
11352 7.249735987
11354 5.470747272
11363 11.22842828
11364 12.47581757
11370 11.31604087
11409 9.763157848
11416 10.55087884
11418 5.190777919
11419 5.997105342
11421 4.719829935
11423 5.096312363

Total number of rows: 16331

Table truncated, full table size 290 Kbytes.




Supplementary file Size Download File type/resource
GSM935108_LR24.2B_Mouse430_2_.CEL.gz 3.6 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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