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Sample GSM372374 Query DataSets for GSM372374
Status Public on Feb 18, 2010
Title 90d Black 1
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 3192.2856 33.9274 G 51.9742 3234.2856 2285.0000 2880.4370 105 11.562445640564 62.2286378749587 43.7088 42.0000 13.4858 188 33.9274
1002 703.1667 7.4732 G 12.5303 743.1667 854.0000 393.4767 78 9.96557521820068 59.3093422021822 42.5110 40.0000 12.8729 188 7.4732
1003 39.4000 0.4187 G 1.3248 80.4000 74.0000 29.1277 55 8.36828422546387 60.6884772768276 43.0549 41.0000 13.1257 188 0.4187
1004 86.3333 0.9175 G 2.0373 128.3333 129.0000 40.3253 63 8.95623207092285 62.9933294378127 44.1209 42.0000 13.9956 188 0.9175
1005 72.3051 0.7685 G 1.7544 116.3051 109.0000 39.8085 59 8.66724491119385 66.2925112474115 46.0989 44.0000 14.8617 188 0.7685
1006 15.6579 0.1664 L 0.9011 57.6579 53.0000 20.7900 38 6.95579624176025 63.9870583727925 44.8421 42.0000 14.6580 177 0.1664
1007 3679.4272 39.1047 G 62.3973 3719.4272 2731.0000 3438.5837 110 11.8345403671265 59.608831780029 41.8571 40.0000 13.0726 188 39.1047
1008 3700.5852 39.3296 G 55.0854 3745.5852 2948.0000 3226.4792 94 10.9400415420532 67.9960081158984 46.5275 45.0000 15.3307 188 39.3296
1010 145.9702 1.5514 G 2.9419 188.9702 190.0000 71.2534 67 9.23618125915527 64.2341440959932 44.2222 43.0000 14.1561 186 1.5514
1012 268.7941 2.8567 G 4.7406 310.7941 318.0000 132.8647 68 9.30485343933105 65.5605033145756 45.3462 42.0000 15.7070 188 2.8567
1013 60.3191 0.6411 G 1.5930 102.3191 92.0000 38.1225 47 7.73577785491943 64.2319907964963 44.7253 42.0000 14.8213 188 0.6411
1014 3775.1226 40.1218 G 55.5312 3820.1226 3828.0000 3312.5276 98 11.1703834533691 68.7924208288169 47.3187 45.0000 15.8616 188 40.1218
1015 3837.2654 40.7822 G 59.3934 3879.2654 3198.0000 3424.3389 98 11.1703834533691 65.3147696604028 44.4564 42.0000 15.5432 155 40.7822
1017 8.4576 0.0899 L 0.7928 51.4576 46.0000 18.8440 59 8.66724491119385 64.910023622969 45.3190 43.0000 14.6067 120 0.0899
1018 16.6075 0.1765 L 0.9301 57.6075 48.0000 28.9146 107 11.6720447540283 61.9391268269931 43.3836 41.0000 13.9594 165 0.1765
1019 13.2778 0.1411 L 0.8708 59.2778 57.0000 30.4764 36 6.7702751159668 68.0761961896155 46.8944 46.0000 14.7175 167 0.1411
1020 21.6087 0.2297 L 0.9834 66.6087 69.0000 28.9058 46 7.65303993225098 67.7358616024104 48.8247 45.0000 15.1572 160 0.2297
1021 3588.0181 38.1332 G 53.4010 3633.0181 2012.0000 3481.8608 110 11.8345403671265 68.0328292403459 47.3036 45.0000 15.3552 174 38.1332
1022 4078.6338 43.3474 G 66.0005 4118.6338 3286.0000 3614.5269 101 11.3400707244873 62.4030228796702 43.3812 40.0000 14.9353 187 43.3474
1024 8.6667 0.0921 L 0.8147 49.6667 48.0000 17.4037 33 6.48204469680786 60.9663571187962 43.4027 41.0000 13.3109 155 0.0921

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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