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Sample GSM935111 Query DataSets for GSM935111
Status Public on Dec 05, 2013
Title PMH exposed to CisPl for 48h, biological rep 2
Sample type RNA
 
Source name primary hepatocytes
Organism Mus musculus
Characteristics cell line: PMH
treatment: CisPl, 7µM
time: 48h
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 CisPl_48h_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 10.11002252
11298 6.884150736
11302 6.470878017
11303 6.232544365
11304 4.363857082
11305 6.558454498
11307 5.06333551
11308 9.345088236
11350 6.91184948
11352 8.122383308
11354 5.479069783
11363 11.43749147
11364 13.33898466
11370 11.29088612
11409 9.833770172
11416 10.12199916
11418 5.036466056
11419 5.824599077
11421 4.494085533
11423 5.259010175

Total number of rows: 16331

Table truncated, full table size 290 Kbytes.




Supplementary file Size Download File type/resource
GSM935111_LR48.2B_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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