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Sample GSM1227013 Query DataSets for GSM1227013
Status Public on Sep 08, 2016
Title Heart_Ctrl_no treatment_ sample 3 (mouse n° 223)
Sample type RNA
 
Channel 1
Source name Heart_Ctrl_no treatment
Organism Mus musculus
Characteristics gender: male
treatment: no treatment
treatment duration: 7 days
tissue: Heart ventricle
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from ventricle samples with the RNeasy Mini Kit (Qiagen S.A) according to the manufacturer's instructions and its quality was assessed with Bioanalyzer 2100 (Agilent technologies)
Label Cy5
Label protocol Labelling of the RNAs weas performed according to Agilent's instruction. Briefly, 100 ng of total RNA + spikes were primed with 1.8µl of T7 promoter primer mix at 70°C for 10 min, then reversed transcribed at 40°C for 2 h in presence of a mix containing first strand buffer, 20 mM DTT, 2 mM DNTP mix and AffinityScript rnase block mix. Reaction was stopped by heating samples at 70° foc 15 min. New synthetized cDNA was then labelled and amplified at 40° for 2h in presence of a mix containing transcription buffer, NTP mix, 20mM DTT, T7 RNA polymerase and CY3-CTP or CY5-CTP.
 
Channel 2
Source name Total RNA pooled from several tissues (liver, brain, heart kidney, spleen), labeled with Cyanine-3, used as reference
Organism Mus musculus
Characteristics tissue composition of reference: liver, brain, heart kidney, spleen
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from ventricle samples with the RNeasy Mini Kit (Qiagen S.A) according to the manufacturer's instructions and its quality was assessed with Bioanalyzer 2100 (Agilent technologies)
Label Cy3
Label protocol Labelling of the RNAs weas performed according to Agilent's instruction. Briefly, 100 ng of total RNA + spikes were primed with 1.8µl of T7 promoter primer mix at 70°C for 10 min, then reversed transcribed at 40°C for 2 h in presence of a mix containing first strand buffer, 20 mM DTT, 2 mM DNTP mix and AffinityScript rnase block mix. Reaction was stopped by heating samples at 70° foc 15 min. New synthetized cDNA was then labelled and amplified at 40° for 2h in presence of a mix containing transcription buffer, NTP mix, 20mM DTT, T7 RNA polymerase and CY3-CTP or CY5-CTP.
 
 
Hybridization protocol 825 ng of Cy5-labelled samples and 825 ng of Cy3-labelled references were incubated at 60° for 30 min in fragmentation buffer. Hybridization buffer was then added, and sample/reference couples (1 couple per microarray) were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential
Scan protocol Scanned on an G2505 Agilent scanner.
Images were quantified using Agilent Feature Extraction Software (version v 10.7.3.1).
Description Sample 3
Hearts were rinsed in cold PBS, frozen in liquid nitrogen, and kept at –80°C.
Data processing Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.Data were processed using genespring software v11.0.
 
Submission date Sep 09, 2013
Last update date Sep 08, 2016
Contact name Smail Messaoudi
E-mail(s) smail.messaoudi@gmail.com
Phone +1 613 562 5800
Organization name University of Ottawa
Department BMI
Street address 451 smyth road
City Ottawa
State/province Ontario
ZIP/Postal code K1H 8M5
Country Canada
 
Platform ID GPL11202
Series (1)
GSE50709 Cardiac aldosterone regulated genes in mice

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

Data table
ID_REF VALUE
GE_BrightCorner -0.5297269
DarkCorner -0.37272596
A_55_P1989846 -0.064120255
A_55_P1991598 -1.1846387
A_55_P2022211 -1.4109155
A_55_P1980764 1.0438842
A_55_P1964375 1.2927294
A_51_P128876 -0.9469072
A_55_P2121042 -0.4486596
A_52_P219230 -1.7723123
A_51_P207591 -1.0823331
A_55_P2131920 2.267169
A_55_P2404223 0.8083438
A_55_P2101944 0.56872755
A_52_P358860 -1.3793344
A_51_P119031 0.38608262
A_51_P309854 -0.619832
A_51_P343900 0.2908983
A_51_P234359 -2.06036
A_51_P487813 -1.7237043

Total number of rows: 39485

Table truncated, full table size 940 Kbytes.




Supplementary file Size Download File type/resource
GSM1227013_US23502393_252665510797_S01_GE2_107_Sep09_1_1.txt.gz 4.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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