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Sample GSM455904 Query DataSets for GSM455904
Status Public on Jun 09, 2010
Title Kidney H2O-treated 03 days replicate 2
Sample type RNA
 
Channel 1
Source name Hupki mouse kidney
Organism Mus musculus
Characteristics tissue: kidney
time point: 3 days
agent: H2O
Treatment protocol Female Hupki mice (2-4 months old) were randomly assigned to dose groups (three animals per time point) and were treated daily with 5 mg/kg body weight aristolochic acid I (AAI) by gavage according to a protocol published previously [Mengs, U. (1988) Tumour induction in mice following exposure to aristolochic acid. Arch Toxicol, 61, 504-505] for 3, 12 or 21 days, respectively. Control animals were treated with vehicle, water only. Mice were killed after 24 h. All animal experiments were carried out under license in accordance with the law, and following local ethical review. Organ sections (kidney and liver) were collected, snap-frozen in liquid nitrogen and stored at -80ºC until further analysis.
Growth protocol Hupki mice (Trp53 tm1/Holl, homozygous for the knock-in TP53 allele harbouring human TP53 sequences in the 129/Sv background) were purchased from The Jackson Laboratory (Bar Harbor, ME, USA) and breed at the Institute of Cancer Research Animal Facility.
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol (Invitrogen) following manufacturer's instructions and purified by Qiagen RNAease mini kit following manufacturer's instructions.
Label Cy5
Label protocol 5 μg of RNA was mixed with 1.2 μl T7 promotor primer (Agilent low RNA input linear amplification kit) and denatured at 65°C for 10 min. After being incubated on ice for 5 min, 8.5 μl cDNA Master Mix (Agilent) was added and the mixture was incubated at at 40°C for 2 hours. The sample was incubated at 65°C for 15 min and placed on ice for 5 min. Then the sample was mixed with Transcription Master Mix (Agilent) and Cy5 (tissue RNA) or Cy3 (UMRR) according to manufature's instuctions. After incubation at 40°C for 2 hours, the sample was purified with RNeasy Mini kit (Qiagen).
 
Channel 2
Source name universal mouse reference RNA
Organism Mus musculus
Characteristics reference: 11 mouse cell lines collection
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol (Invitrogen) following manufacturer's instructions and purified by Qiagen RNAease mini kit following manufacturer's instructions.
Label Cy3
Label protocol 5 μg of RNA was mixed with 1.2 μl T7 promotor primer (Agilent low RNA input linear amplification kit) and denatured at 65°C for 10 min. After being incubated on ice for 5 min, 8.5 μl cDNA Master Mix (Agilent) was added and the mixture was incubated at at 40°C for 2 hours. The sample was incubated at 65°C for 15 min and placed on ice for 5 min. Then the sample was mixed with Transcription Master Mix (Agilent) and Cy5 (tissue RNA) or Cy3 (UMRR) according to manufature's instuctions. After incubation at 40°C for 2 hours, the sample was purified with RNeasy Mini kit (Qiagen).
 
 
Hybridization protocol Test sample (Cy5-labelled) and reference (Cy3-labelled) were mixed and hybridised with Gene Expression Hybridization Kit (Agilent) on Agilent whole genome mouse 44k arrays following manufacturer's instructions. The arrays were incuated in Agilent SureHyb-enabled hybridization chambers, which was placed in the oven for 18 hours ( 65°C; 10 rpm).
Scan protocol After hybridisation, the arrays were washed by Agilent Gene Expression Wash Buffer following the instructions. The arrays were scanned with a Axon 4000B scanner at wavelength 635nm and 532nm.
Description KICON03DG14C6
Data processing The images were analysed with BlueFuse software to extract expression values, then all data were loaded into GeneSpring V7.2 software. The data were LOWESS normalised and natural log-ratios were used for t-test and other analyses. Normalised ratios were used for fold-change analysis.
 
Submission date Sep 24, 2009
Last update date Jun 09, 2010
Contact name Ian Giddings
E-mail(s) ian.giddings@icr.ac.uk, daniel.brewer@icr.ac.uk
Phone +44 20 8722 4293
Fax +44 20 8722 4141
URL http://www.crukdmf.icr.ac.uk
Organization name Institute of Cancer Research
Department Section of Molecular Carcinogenesis
Lab CANCER RESEARCH UK DNA Microarray Facility
Street address 15 Cotswold Road
City Sutton
State/province Surrey
ZIP/Postal code SM2 5NG
Country United Kingdom
 
Platform ID GPL7202
Series (1)
GSE18246 Gene expression changes induced by the human aristolochic acid I in renal and hepatic tissue of mice

Data table header descriptions
ID_REF
VALUE Normalized natural log ratio (Cy5/Cy3) representing test/reference.

Data table
ID_REF VALUE
A_51_P100021 -1.4804184
A_51_P100034 0.59518385
A_51_P100052 -0.2026469
A_51_P100063 1.2352033
A_51_P100084 0.2738366
A_51_P100099 -0.6770917
A_51_P100155 -0.47786084
A_51_P100174 -1.3214831
A_51_P100181 -0.72210556
A_51_P100218
A_51_P100227 -1.3586949
A_51_P100238 0.3406065
A_51_P100246 -0.49400643
A_51_P100289 -0.7403295
A_51_P100298 -0.066246614
A_51_P100309
A_51_P100327 -0.6913197
A_51_P100347 1.2956867
A_51_P100379
A_51_P100428 -0.7694039

Total number of rows: 41266

Table truncated, full table size 826 Kbytes.




Supplementary file Size Download File type/resource
GSM455904.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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