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Sample GSM488099 Query DataSets for GSM488099
Status Public on Dec 23, 2009
Title Qinchuan cattle, longuissimus dorsi muscle at 36 months, biological rep CM1
Sample type RNA
 
Source name Qinchuan cattle, longuissimus dorsi muscle, castrated male, 36 months
Organism Bos taurus
Characteristics breed: Qinchuan
tissue: longuissimus dorsi muscle
gender: castrated male
age: 36 months
Treatment protocol Cattle were slaughtered at 36 months of age. Longuissimus dorsi tissues were taken adjacent to the 12th section of the Longuissimus dorsi muscle, immediately frozen in liquid nitrogen, and conserved at -80C
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Bovine Genome arrays using ArrayAffymetrix® GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix® GeneChip® Scanner 3000.
Description Gene expression data from Qinchuan cattle longuissimus dorsi muscle at 36 months.
Data processing The data were analyzed with Affymetrix® GeneChip® Operating Software Version1.4 (GCOS1.4) using Affymetrix default analysis settings. The trimmed mean target intensity of each array was arbitrarily set to 500.
 
Submission date Dec 19, 2009
Last update date Dec 22, 2009
Contact name Yingying Zhang
E-mail(s) zyysingbird@yahoo.com.cn
Organization name National Beef Cattle Improvement Center
Street address No.22 Xinong Road, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China.
City Yangling
ZIP/Postal code 712100
Country China
 
Platform ID GPL2112
Series (1)
GSE19586 Expression data from the longuissimus dorsi muscle of Qinchuan cattle, Qinghai yak and Guangxi buffalo at 36 months

Data table header descriptions
ID_REF
VALUE GCOS1.4-calculated signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 378.171 P 0.000095
AFFX-BioB-M_at 418.761 P 0.000044
AFFX-BioB-3_at 332.891 P 0.000052
AFFX-BioC-5_at 862.583 P 0.000052
AFFX-BioC-3_at 1236.43 P 0.000044
AFFX-BioDn-5_at 2299.8 P 0.000044
AFFX-BioDn-3_at 4025.57 P 0.000081
AFFX-CreX-5_at 10780.2 P 0.000052
AFFX-CreX-3_at 12019.8 P 0.000044
AFFX-DapX-5_at 198.572 P 0.00007
AFFX-DapX-M_at 937.45 P 0.000297
AFFX-DapX-3_at 1511.7 P 0.000044
AFFX-LysX-5_at 81.5273 P 0.00007
AFFX-LysX-M_at 151.871 P 0.00034
AFFX-LysX-3_at 371.096 P 0.000044
AFFX-PheX-5_at 90.757 P 0.00011
AFFX-PheX-M_at 232.747 P 0.000581
AFFX-PheX-3_at 288.63 P 0.000052
AFFX-ThrX-5_at 81.532 P 0.003212
AFFX-ThrX-M_at 100.783 P 0.000225

Total number of rows: 24128

Table truncated, full table size 837 Kbytes.




Supplementary file Size Download File type/resource
GSM488099.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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