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Sample GSM372379 Query DataSets for GSM372379
Status Public on Feb 18, 2010
Title 90d Yellow 3
Sample type RNA
 
Source name ovary
Organism Mus musculus
Characteristics tissue: ovary
gender: female
age: 90 days
strain: C56BL/6J Ay/a
treatment 1: Antide on days 1 and 4
dose: 10 microg/g
treatment 2: equine chorionic gonadotropin
dose: 1 IU/5g body weight
tissue collection: day 7
Extracted molecule total RNA
Extraction protocol The ovaries were collected into RNAlater (Ambion) and frozen. The RNAlater was blotted and the ovaries were homogenized in 1 ml TRI reagent (MRC). Bromochloropropane and sodium acetate were added to the homogenate and the sample was centrifuged to separate the phases. The RNA-containing layer was removed and the RNA purified on an RNeasy extraction column (Qiagen). The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen). The purity and quantity of the total RNA was evaluated with the RNA 6000 NanoLabChip in an Agilent Bioanalyzer.
Label Alexa-647
Label protocol http://www4.amershambiosciences.com/APTRIX/upp00919.nsf/Content/WD%3ACodeLink+Gene+E%28270813678-B500%29?OpenDocument&hometitle
 
Hybridization protocol http://www4.amershambiosciences.com/APTRIX/upp00919.nsf/Content/WD%3ACodeLink+Gene+E%28270810969-B500%29?OpenDocument&hometitle
Scan protocol http://www4.amershambiosciences.com/APTRIX/upp00919.nsf/Content/WD%3AScanning+CodeLi%28248345081-B500%29?OpenDocument&hometitle
Description IACUC approval was obtained for all animal treatments.
Data processing global median normalization, CodeLink Expression Analysis 4.1.0.4163
 
Submission date Feb 19, 2009
Last update date Feb 23, 2009
Contact name Kathleen M Eyster
E-mail(s) Kathleen.Eyster@usd.edu
Organization name University of South Dakota
Department Basic Biomedical Sciences
Street address 414 E. Clark St.
City Vermillion
State/province SD
ZIP/Postal code 57069
Country USA
 
Platform ID GPL2897
Series (1)
GSE14937 Altered ovarian gene expression in the lethal yellow mouse

Data table header descriptions
ID_REF
Raw_intensity Raw signal intensity value
VALUE Median normalized signal intensity value with flagged values (Quality_flag = M) removed
Quality_flag CodeLink quality flag
Signal_strength Signal strength
Spot_mean Spot mean
Spot_median Spot median
Spot_stdev Spot standard deviation
Spot_area Spot area
Spot_diameter Spot diameter
Spot_noise_level Spot noise level
Bkgd_mean Background mean
Bkgd_median Background median
Bkgd_stdev Background standard deviation
Bkgd_area Background area
UNF_VALUE Median normalized signal intensity value

Data table
ID_REF Raw_intensity VALUE Quality_flag Signal_strength Spot_mean Spot_median Spot_stdev Spot_area Spot_diameter Spot_noise_level Bkgd_mean Bkgd_median Bkgd_stdev Bkgd_area UNF_VALUE
1001 3531.0801 34.5326 G 61.1345 3569.0801 3153.0000 3010.5508 100 11.2837915420532 58.380822401952 41.5165 38.0000 13.5872 188 34.5326
1002 753.4535 7.3685 G 13.4605 793.4535 889.0000 444.2813 86 10.4641580581665 58.9467910024407 42.1374 40.0000 12.6312 188 7.3685
1003 40.3125 0.3942 G 1.3479 81.3125 76.0000 27.2658 48 7.81764030456543 60.3259596254848 43.0934 41.0000 12.8840 188 0.3942
1004 111.1351 1.0869 G 2.4838 151.1351 152.0000 55.7895 74 9.70668506622314 60.8472185560269 41.6209 40.0000 13.8981 188 1.0869
1005 54.1129 0.5292 G 1.5973 97.1129 93.0000 31.3755 62 8.88486671447754 60.7981708650888 43.0000 43.0000 11.8654 186 0.5292
1006 8.0682 0.0789 L 0.8310 49.0682 46.0000 16.9302 88 10.5851345062256 59.0486580004605 42.6743 41.0000 12.0324 181 0.0789
1007 3705.9341 36.2426 G 61.3647 3746.9341 3580.0000 3287.7051 106 11.617374420166 61.0601120873544 43.0604 41.0000 13.3734 188 36.2426
1008 3597.8660 35.1857 G 61.1158 3638.8660 3032.0000 3125.0767 97 11.1132459640503 59.540515814762 43.0190 41.0000 12.3603 164 35.1857
1010 160.0556 1.5653 G 3.1832 205.0556 210.0000 70.7046 72 9.57461452484131 64.4185364786065 45.5244 45.0000 12.9457 170 1.5653
1012 298.4776 2.9190 G 5.2850 341.4776 333.0000 138.5163 67 9.23618125915527 64.6120847523674 45.3111 43.0000 14.4081 186 2.9190
1013 51.4909 0.5036 G 1.4893 93.4909 88.0000 26.5130 55 8.36828422546387 62.7770000389826 44.5769 42.0000 13.8513 188 0.5036
1014 3754.1914 36.7145 G 60.1863 3797.1914 3730.0000 3119.6594 94 10.9400415420532 63.0906127537089 43.5220 43.0000 13.3937 188 36.7145
1015 3688.4902 36.0720 G 59.6022 3728.4902 3110.0000 3331.4006 102 11.396071434021 62.5562883575957 43.3132 40.0000 15.0375 188 36.0720
1017 13.5306 0.1323 L 0.9471 53.5306 51.0000 17.7305 49 7.89865398406982 56.5220877058598 41.1779 40.0000 11.0147 169 0.1323
1018 34.8444 0.3408 G 1.2542 74.8444 73.0000 17.7913 45 7.56939744949341 59.6772035695262 42.8626 40.0000 13.1181 188 0.3408
1019 30.6957 0.3002 G 1.1976 72.6957 68.0000 23.6624 46 7.65303993225098 60.6996710077086 43.9887 42.0000 12.4664 183 0.3002
1020 25.9412 0.2537 G 1.1278 65.9412 62.0000 31.4732 51 8.0582389831543 58.4690434327818 42.4407 40.0000 12.3127 183 0.2537
1021 3553.9082 34.7558 G 61.3050 3593.9082 2622.0000 3315.8586 109 11.7806243896484 58.6234288131101 42.2582 40.0000 12.4156 188 34.7558
1022 3708.7524 36.2702 G 61.9944 3749.7524 2889.0000 3359.5999 105 11.562445640564 60.4853375336531 42.7747 41.0000 12.9902 188 36.2702
1024 4.5795 0.0448 L 0.7201 44.5795 40.0000 14.3112 88 10.5851345062256 61.9062783517178 43.8280 40.0000 14.6042 192 0.0448

Total number of rows: 36227

Table truncated, full table size 4576 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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