NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1077031 Query DataSets for GSM1077031
Status Public on Feb 03, 2013
Title LD_Wagyu_3m
Sample type RNA
 
Source name Wagyu by Hereford LD muscle, 3 months postnatal
Organism Bos taurus
Characteristics cross: Wagyu by Hereford
age: 3 months postnatal
tissue: LD muscle
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol following the manufacturer's instructions
Label Cy3, Cy5
Label protocol Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential
 
Hybridization protocol Scanned on an Agilent G2565AA scanner.
Scan protocol Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).
Description Sample: W03M
Sample replicates: W03M_1, W03M_2, W03M_3, W03M_4
Raw files are listed in 'README_SampleReps_RawFiles_CyDyes.txt' which is linked as supplementary file on the Series record.
Data processing Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Further, a mixed model normalisation method was applied and the BLUP solution for the gene by condition interaction was used as the normalized mean expression of each gene in each experimental condition.
We used a loop experimental design, and in these cases computing red/green ratios are not optimal. Instead we computed the intensity of the red and the intensity of the green signals.
 
Submission date Feb 02, 2013
Last update date Feb 03, 2013
Contact name Nicholas James Hudson
E-mail(s) [email protected]
Phone +61 +7 3214 2212
Fax +61 +7 3214 2200
Organization name CSIRO
Department Animal, Food and Health Sciences
Lab Systems and Computational Biology
Street address 306 Carmody Road
City Brisbane
ZIP/Postal code 4075
Country Australia
 
Platform ID GPL9712
Series (1)
GSE44030 Inferring the in vivo cellular program of developing bovine muscle from expression data

Data table header descriptions
ID_REF
VALUE Normalized mean expression (log2) intensity

Data table
ID_REF VALUE
A_73_100002 10.6989
A_73_100004 4.5068
A_73_100005 12.2775
A_73_100006 12.2792
A_73_100009 10.3068
A_73_100010 6.51186
A_73_100011 7.63781
A_73_100012 8.87435
A_73_100013 3.92598
A_73_100015 6.79139
A_73_100016 12.7713
A_73_100017 3.552
A_73_100018 4.72607
A_73_100019 5.67394
A_73_100021 14.826
A_73_100023 8.8205
A_73_100024 13.8899
A_73_100025 4.7821
A_73_100026 10.0142
A_73_100028 5.7285

Total number of rows: 21475

Table truncated, full table size 417 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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