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Sample GSM935107 Query DataSets for GSM935107
Status Public on Dec 05, 2013
Title PMH exposed to PBS for 24h, biological rep 1
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_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 13.31241894
11298 7.06710362
11302 6.420227399
11303 8.137692829
11304 4.758445037
11305 6.925410923
11307 5.230973679
11308 9.166177984
11350 6.565085914
11352 7.113226923
11354 5.550666728
11363 11.26170316
11364 12.66237552
11370 11.34695851
11409 9.844306274
11416 10.40901983
11418 5.254809065
11419 5.787108232
11421 4.708169266
11423 5.093111695

Total number of rows: 16331

Table truncated, full table size 290 Kbytes.




Supplementary file Size Download File type/resource
GSM935107_LR24.1B_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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