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Sample GSM935115 Query DataSets for GSM935115
Status Public on Dec 05, 2013
Title PMH exposed to PBS for 48h, biological rep 3
Sample type RNA
 
Source name primary hepatocytes
Organism Mus musculus
Characteristics cell line: PMH
treatment: PBS, 0.5%
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 PBS_48h_Ex3
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 12.85376363
11298 7.124240534
11302 6.426019929
11303 7.616429483
11304 4.888440926
11305 6.603500515
11307 5.21890767
11308 9.564236703
11350 6.760982036
11352 7.498975086
11354 5.461080706
11363 11.3864901
11364 12.54135819
11370 11.06281144
11409 10.02671816
11416 10.54166537
11418 5.179581062
11419 5.615751373
11421 4.454707888
11423 5.262997373

Total number of rows: 16331

Table truncated, full table size 290 Kbytes.




Supplementary file Size Download File type/resource
GSM935115_LR24.3A_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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