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Sample GSM372368 Query DataSets for GSM372368
Status Public on Feb 18, 2010
Title 180d Black 1
Sample type RNA
 
Source name ovary
Organism Mus musculus
Characteristics tissue: ovary
gender: female
age: 180 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 12420.9756 94.8598 G 145.9105 12474.9756 2530.0000 14707.0098 161 14.3175268173218 85.4974630293748 55.2333 54.0000 20.9983 124 94.8598
1002 1368.0000 10.4475 G 16.9934 1418.0000 1613.0000 674.0753 89 10.6451082229614 83.4439799067395 52.9852 50.0000 22.2960 139 10.4475
1003 74.8769 0.5718 G 1.5352 120.8769 113.0000 46.5616 65 9.09728336334229 78.7385850151721 48.8690 46.0000 21.8257 149 0.5718
1004 108.7973 0.8309 G 1.9071 158.7973 156.0000 56.8626 74 9.70668506622314 83.2675365463679 53.6374 50.0000 22.1784 188 0.8309
1005 89.9524 0.6870 G 1.7089 136.9524 135.0000 54.0119 63 8.95623207092285 80.1403389523102 53.2363 47.0000 22.0936 188 0.6870
1006 38.6341 0.2951 G 1.0925 84.6341 85.0000 34.1380 41 7.22515201568604 77.4704596160188 50.6464 46.0000 20.9803 187 0.2951
1007 14928.9092 114.0131 G 174.9198 14978.9092 4067.0000 17493.5508 154 14.0028171539307 85.6330037523297 55.7250 50.0000 23.7553 124 114.0131
1008 15313.8057 116.9526 G 178.6630 15365.8057 5145.0000 17364.3672 144 13.5405502319336 86.0044040157969 56.8351 52.0000 22.6696 101 116.9526
1010 325.7500 2.4878 G 5.0720 372.7500 376.0000 125.7597 76 9.83698177337646 73.4913043049071 51.4714 47.0000 17.6609 144 2.4878
1012 631.4048 4.8221 G 8.0206 682.4048 741.0000 272.0320 84 10.3417663574219 85.0813176527438 54.5249 51.0000 22.7209 187 4.8221
1013 62.5000 0.4773 G 1.3856 110.5000 105.0000 46.7349 58 8.59348011016846 79.7503770100607 52.1483 48.0000 21.1669 188 0.4773
1014 11711.9053 89.4446 G 150.9639 11758.9053 3464.0000 13815.6689 158 14.1835060119629 77.8921836894435 50.9153 47.0000 20.5948 122 89.4446
1015 12510.6982 95.5451 G 159.7710 12558.6982 4709.0000 13913.4922 139 13.303394317627 78.6043459139288 52.8086 48.0000 20.4029 168 95.5451
1017 7.9294 0.0606 L 0.6875 56.9294 52.0000 23.6020 85 10.4031419754028 82.8100227556596 52.9202 49.0000 22.5400 194 0.0606
1018 40.5079 0.3094 G 1.0971 91.5079 92.0000 43.3307 63 8.95623207092285 83.4108113781974 53.7712 51.0000 21.6072 122 0.3094
1019 65.5769 0.5008 G 1.3270 114.5769 112.0000 48.0130 52 8.1368579864502 86.3419168815391 54.8956 49.0000 24.8946 188 0.5008
1020 40.2000 0.3070 G 1.0657 88.2000 83.0000 30.3770 40 7.13649654388428 82.7611633439539 53.4560 48.0000 23.1741 188 0.3070
1021 13775.5156 105.2046 G 152.2795 13829.5156 9157.0000 14275.5986 130 12.8655023574829 90.8166722579678 57.9011 54.0000 24.5444 188 105.2046
1022 11386.5615 86.9600 G 134.8749 11436.5615 2252.0000 13840.4824 162 14.3619222640991 84.7938504570739 55.5167 50.0000 23.1959 124 86.9600
1024 7.2759 0.0556 L 0.6495 56.2759 50.0000 25.4706 29 6.07650756835938 86.6436596341841 56.0659 49.0000 25.0958 188 0.0556

Total number of rows: 36227

Table truncated, full table size 4595 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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