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Sample GSM1077025 Query DataSets for GSM1077025
Status Public on Feb 03, 2013
Title LD_Piedmontese_25m
Sample type RNA
 
Source name Piedmontese by Hereford LD muscle, 25 months postnatal
Organism Bos taurus
Characteristics cross: Piedmontese by Hereford
age: 25 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: P25M
Sample replicates: P25M_1, P25M_2, P25M_3, P25M_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) nick.hudson@csiro.au
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 10.5104
A_73_100004 4.49668
A_73_100005 12.2325
A_73_100006 12.1389
A_73_100009 9.4333
A_73_100010 6.7393
A_73_100011 6.89018
A_73_100012 9.48876
A_73_100013 4.48794
A_73_100015 6.51817
A_73_100016 13.2986
A_73_100017 3.0556
A_73_100018 5.00793
A_73_100019 5.25945
A_73_100021 15.0604
A_73_100023 9.18511
A_73_100024 13.6321
A_73_100025 4.77148
A_73_100026 10.3264
A_73_100028 7.39242

Total number of rows: 21475

Table truncated, full table size 417 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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