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Sample GSM277586 Query DataSets for GSM277586
Status Public on Aug 01, 2008
Title Patient fibroblast (P1.gpr)
Sample type RNA
 
Channel 1
Source name Total RNA from patient fibroblast labeled with Cyanine-5 (red)
Organism Homo sapiens
Characteristics fibroblast
Treatment protocol For experiments, confluent cell were harvested using 0.05 % trypsine and 0.02 % EDTA
Growth protocol Skin fibroblasts were cultured in the Dulbecco’s modified Eagle’s medium supplemented by 10 % fetal calf serum, 20mM HEPES pH 7.5, 0.2 % NaHCO3 and gentamycin 0.02 mg/ml at 37°C and 5 % CO2 in air
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol following manufacturer's instructions.
Label Cy5
Label protocol 500 ng of total RNA was reverse transcripted to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).
 
Channel 2
Source name Total RNA from reference HeLa cell lines labeled with Cyanine-3 (green)
Organism Homo sapiens
Characteristics HeLa
Treatment protocol For experiments, confluent cell were harvested using 0.05 % trypsine and 0.02 % EDTA
Growth protocol Skin fibroblasts were cultured in the Dulbecco’s modified Eagle’s medium supplemented by 10 % fetal calf serum, 20mM HEPES pH 7.5, 0.2 % NaHCO3 and gentamycin 0.02 mg/ml at 37°C and 5 % CO2 in air
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol following manufacturer's instructions.
Label Cy3
Label protocol 500 ng of total RNA was reverse transcripted to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).
 
 
Hybridization protocol 825ng of Cy3 and Cy5 labelled aRNA were hybridized competitively for 17 hrs in a 65° C, according to the manufacturer's recommnded protocol (Two-Color Microarray-Based Gene expression Analysis, Agilent) .
Scan protocol The hybridized slides were scanned with GenePix 4200A scanner (Axon Instrument, Union City, CA) with PMT gains adjusted to obtain highest intensity unsaturated images. Gene PixPro software (Axon Instruments) was used for image analysis the of TIFF files, as generated by the scanner.
Description none
Data processing Data from individual arrays were background corrected (using normexp method), log transformed and normalized using Loess and G-quantile functions. Normalization was performed in R statistic environment using Limma package
 
Submission date Mar 26, 2008
Last update date Jun 26, 2008
Contact name Viktor Stranecky
Organization name Charles University
Department 1st Faculty of Medicine
Lab Institute of inherited metabolic disorders
Street address Ke Karlovu 2
City Prague
ZIP/Postal code 128 00
Country Czech Republic
 
Platform ID GPL4133
Series (1)
GSE10956 Gene expression analysis in 13 patients with mitochondrial ATP synthase deficiency (Agilent)

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Cy5/Cy3)

Data table
ID_REF VALUE
23011 1.55
10328 -0.17
25051 -0.46
28887 0.11
10813 -1.75
10308 0.12
29524 0.06
36849 0.79
38433 -0.69
36162 0.67
27803 -4.28
19264 0.80
4207 0.06
1029 -0.52
22079 0.02
41614 0.66
25262 -2.17
4766 -0.25
41459 -0.07
17897 0.63

Total number of rows: 24730

Table truncated, full table size 271 Kbytes.




Supplementary file Size Download File type/resource
GSM277586.gpr.gz 6.2 Mb (ftp)(http) GPR
Processed data included within Sample table

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