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Sample GSM935113 Query DataSets for GSM935113
Status Public on Dec 05, 2013
Title PMH exposed to PBS for 48h, biological rep 1
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_Ex1
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 12.96049508
11298 7.169785472
11302 6.115309383
11303 7.550413052
11304 5.075856669
11305 6.81754017
11307 4.939064551
11308 9.218097338
11350 6.866537977
11352 7.489000979
11354 5.463382569
11363 11.53951363
11364 12.51031017
11370 11.35774463
11409 10.30801893
11416 10.25509639
11418 5.504847129
11419 5.994897112
11421 4.627829733
11423 5.153044386

Total number of rows: 16331

Table truncated, full table size 290 Kbytes.




Supplementary file Size Download File type/resource
GSM935113_LR48.1B_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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