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Sample GSM82403 Query DataSets for GSM82403
Status Public on Aug 01, 2006
Title P63 Non failing heart biopsy
Sample type RNA
 
Channel 1
Source name heart, middle septum
Organism Homo sapiens
Characteristics Non failing
Biomaterial provider Department of Medicine I, University Hospital Grosshadern, Ludwig-Maximilians-University, Munich, Germany
Treatment protocol none
Growth protocol none
Extracted molecule total RNA
Extraction protocol total RNA was extracted using Qiagen RNeasy Midi Kit reagents; 2µg total RNA was amplified one round based on T7 RNA Polymerase (Ambion Message Amplification Kit Reagents, 6h IVT)
Label Cy3
Label protocol direct fluorescent labelling of 2 µg amplified RNA, anneling of 0.5µg Random Primer and reverse-transcribed into cDNA with Superscript III reverse transcriptase for 1h at 42°C in the presence of 0.4 mM dGTP, 0.4 mM dATP, 0.4 mM dTTP, 0.24 mM dCTP, 0.125 mM Cy3-dCTP. After hydrolysis of RNA in 0.2 M NaOH, Cy3-labeled probes were purified with Microcon YM-30 column.
 
Channel 2
Source name Universal human reference RNA (Stratagene), one round amplified
Organism Homo sapiens
Characteristics common reference sample
Biomaterial provider Stratagene
Treatment protocol none
Growth protocol none
Extracted molecule total RNA
Extraction protocol 2µg total RNA was amplified one round based on T7 RNA Polymerase (Ambion Message Amplification Kit Reagents, 6h IVT)
Label Cy5
Label protocol direct fluorescent labelling of 2 µg amplified RNA, anneling of 0.5µg Random Primer and reverse-transcribed into cDNA with Superscript III reverse transcriptase for 1h at 42°C in the presence of 0.4 mM dGTP, 0.4 mM dATP, 0.4 mM dTTP, 0.24 mM dCTP, 0.125 mM Cy5-dCTP. After hydrolysis of RNA in 0.2 M NaOH, Cy5-labeled probes were purified with Microcon YM-30 column.
 
 
Hybridization protocol ch1 and ch2 together are solved in 50 µl 1x DIG-Easy hybridization buffer (Roche Diagnostics, Mannheim, Germany), containing 10x Denhardt’s solution and 2 ng/µl Cot1-DNA (Invitrogen); sample was denaturated at 65°C for 2min, hybridzation of arrays were performed in Corning chambers 14h at 37°C; slides were washed twice in 1xSSC+0.1SDS and once in 0.1xSSC+ 0.1SDS before air pressure drying and scanning.
Scan protocol arrays were scanned with the GenePix 4000B microarray scanner and analyzed using GenePix Pro 4.1 software (Axon Instruments)
Description P63 Non failing heart biopsy
Data processing raw data processing was performed using ArrayMagic (Buness et al., 2005) and VSN normalization method; after removal of bad quality spots, two hybridizations of this sample were merged; generalized log2 ratios from 30498 cDNA clones were given in the data table.
 
Submission date Nov 08, 2005
Last update date Jun 06, 2006
Contact name Ruprecht Kuner
Organization name German Cancer Research Center and National Center of Tumor Diseases
Department Molecular Genetics
Lab Unit Cancer Genome Research
Street address Im Neuenheimer Feld 460
City Heidelberg
ZIP/Postal code 69120
Country Germany
 
Platform ID GPL3050
Series (1)
GSE3586 Dilated Cardiomyopathy and Non Failing Septal Biopsies

Data table header descriptions
ID_REF
VALUE generalized log2 ratios

Data table
ID_REF VALUE
IMAGp998O01132 -0.504495915
IMAGp998K14130 -0.835688736
IMAGp998J03131 -0.306367816
IMAGp998C13133 -0.157674673
IMAGp998A02134 -0.448819021
IMAGp998M11127 -1.289660408
IMAGp998J20124 -0.200270979
IMAGp998P01124 -1.12706206
IMAGp998F13119 -1.001754541
IMAGp998B05118 0.275213037
IMAGp998E20124 0.589157234
IMAGp998F04123 -0.127776159
IMAGp998P1497 -0.260542526
IMAGp998N04119 -1.401246991
IMAGp998B01111 0.597649835
IMAGp998I16115 0.372407989
IMAGp998G03117 -0.4553078
IMAGp998B15114 -0.600172017
IMAGp998K1984 -0.31322858
IMAGp998O0781 -0.353998037

Total number of rows: 30498

Table truncated, full table size 828 Kbytes.




Supplementary file Size Download File type/resource
GSM82403_1.gpr.gz 3.1 Mb (ftp)(http) GPR
GSM82403_2.gpr.gz 3.1 Mb (ftp)(http) GPR

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