NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1227015 Query DataSets for GSM1227015
Status Public on Sep 08, 2016
Title Heart_Ctrl _no treatment_ sample 5 (mouse n° 215)
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 5
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 -0.42785445
DarkCorner -0.06105659
A_55_P1989846 -0.17219204
A_55_P1991598 -0.11473708
A_55_P2022211 -0.98912346
A_55_P1980764 1.4767199
A_55_P1964375 0.98894787
A_51_P128876 -1.0091944
A_55_P2121042 -0.11012734
A_52_P219230 -0.15290977
A_51_P207591 -1.0681925
A_55_P2131920 2.8199053
A_55_P2404223 0.61702245
A_55_P2101944 0.59739596
A_52_P358860 -1.7801399
A_51_P119031 0.4798126
A_51_P309854 -0.7140751
A_51_P343900 0.27414992
A_51_P234359 -1.9393369
A_51_P487813 -1.1397991

Total number of rows: 39485

Table truncated, full table size 947 Kbytes.




Supplementary file Size Download File type/resource
GSM1227015_US23502393_252665510799_S01_GE2_107_Sep09_1_1.txt.gz 4.2 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap