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Sample GSM372375 Query DataSets for GSM372375
Status Public on Feb 18, 2010
Title 90d Black 2
Sample type RNA
 
Source name ovary
Organism Mus musculus
Characteristics tissue: ovary
gender: female
age: 90 days
strain: C56BL/6J a/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 3232.1238 27.2380 G 52.0007 3274.1238 2856.0000 2770.0061 97 11.1132459640503 62.9630550904419 43.6264 42.0000 13.9754 188 27.2380
1002 1065.5488 8.9797 G 19.2009 1103.5488 1253.0000 592.2293 82 10.2179079055786 57.4737357817478 41.3462 38.0000 12.9825 188 8.9797
1003 32.7037 0.2756 G 1.2681 70.7037 65.0000 27.3114 54 8.29185962677002 55.7573249299233 39.8736 38.0000 11.8382 188 0.2756
1004 105.8508 0.8920 G 2.4799 144.8508 139.0000 51.2423 67 9.23618125915527 58.4089709846242 40.4945 39.0000 12.9393 188 0.8920
1005 92.7500 0.7816 G 2.3027 131.7500 127.0000 47.1162 64 9.02703380584717 57.2147485784567 41.6154 39.0000 12.1432 188 0.7816
1006 11.2778 0.0950 L 0.8743 53.2778 53.0000 17.5430 36 6.7702751159668 60.9396837759483 43.9819 42.0000 12.6265 172 0.0950
1007 3420.6125 28.8264 G 59.0853 3459.6125 2694.0000 3173.5942 111 11.8882122039795 58.5528619840346 40.8517 39.0000 13.0352 188 28.8264
1008 3470.3438 29.2455 G 59.5064 3510.3438 3519.0000 3066.2678 96 11.0558128356934 58.9909936083486 43.2901 40.0000 12.6607 168 29.2455
1010 183.3750 1.5453 G 3.8659 222.3750 220.0000 96.0006 72 9.57461452484131 57.521971228911 40.5682 39.0000 12.3480 182 1.5453
1012 403.0548 3.3966 G 7.0716 444.0548 496.0000 204.2339 73 9.64087581634521 62.7937435680693 44.2912 41.0000 14.5292 188 3.3966
1013 54.8000 0.4618 G 1.5265 94.8000 92.0000 32.3145 60 8.74038791656494 62.1013099967452 42.5254 40.0000 14.7342 183 0.4618
1014 3678.6138 31.0006 G 61.3839 3720.6138 3267.0000 3212.8198 101 11.3400707244873 60.6121903677151 43.1044 42.0000 12.4081 188 31.0006
1015 3569.6572 30.0824 G 61.4100 3607.6572 2976.0000 3318.2961 105 11.562445640564 58.7470609253271 42.3556 38.0000 13.8314 186 30.0824
1017 6.1296 0.0517 L 0.8014 51.1296 48.0000 18.3536 54 8.29185962677002 63.8015312732893 46.3000 45.0000 12.5344 124 0.0517
1018 38.7719 0.3267 G 1.3331 79.7719 79.0000 29.7386 57 8.51907634735107 59.8407940338719 43.0800 41.0000 12.5605 156 0.3267
1019 42.3818 0.3572 G 1.3491 83.3818 81.0000 18.3981 55 8.36828422546387 61.8063238567586 43.7955 41.0000 13.8709 182 0.3572
1020 28.1277 0.2370 G 1.1175 72.1277 75.0000 24.3796 47 7.73577785491943 64.543256360125 45.3132 44.0000 13.6955 188 0.2370
1021 3689.6147 31.0933 G 62.9081 3729.6147 2548.0000 3479.1655 109 11.7806243896484 59.2867424325573 42.0769 40.0000 12.8578 188 31.0933
1022 3708.5505 31.2529 G 59.0996 3750.5505 3089.0000 3523.9841 109 11.7806243896484 63.4614704887192 44.6961 42.0000 14.3076 187 31.2529
1024 5.2281 0.0441 L 0.7340 44.2281 43.0000 14.8891 57 8.51907634735107 60.2569667440156 42.8750 39.0000 14.1713 124 0.0441

Total number of rows: 36227

Table truncated, full table size 4574 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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