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Sample GSM372378 Query DataSets for GSM372378
Status Public on Feb 18, 2010
Title 90d Yellow 2
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 2999.2478 28.9871 G 51.6935 3038.2478 2526.0000 2693.7681 109 11.7806243896484 58.7742882386917 41.7582 39.0000 13.1829 188 28.9871
1002 801.9500 7.7507 G 14.1883 840.9500 916.0000 395.7058 80 10.0925302505493 59.2707466601727 41.4945 39.0000 13.5138 188 7.7507
1003 33.8364 0.3270 G 1.2411 72.8364 73.0000 25.0880 55 8.36828422546387 58.6848086919439 41.4033 39.0000 13.1232 187 0.3270
1004 112.1806 1.0842 G 2.6303 152.1806 140.0000 59.3437 72 9.57461452484131 57.8564774101128 41.5989 40.0000 11.9043 188 1.0842
1005 59.5000 0.5751 G 1.7122 97.5000 91.0000 30.5671 62 8.88486671447754 56.9459419340123 41.4966 38.0000 12.6306 149 0.5751
1006 6.4146 0.0620 L 0.7978 46.4146 43.0000 17.5026 41 7.22515201568604 58.1805392927737 40.9437 40.0000 12.1204 166 0.0620
1007 3105.9727 30.0185 G 54.9365 3145.9727 2868.0000 2756.3076 110 11.8345403671265 57.265653815828 42.2198 40.0000 11.5104 188 30.0185
1008 3033.5000 29.3181 G 51.2648 3073.5000 2951.0000 2575.9138 98 11.1703834533691 59.953363596019 42.1319 40.0000 13.3022 188 29.3181
1010 152.4118 1.4730 G 3.0381 192.4118 202.0000 72.4238 68 9.30485343933105 63.333063740795 44.1897 40.0000 15.5554 180 1.4730
1012 297.6324 2.8766 G 5.6134 338.6324 357.0000 135.8117 68 9.30485343933105 60.3260611862724 43.4011 41.0000 12.8840 188 2.8766
1013 44.2745 0.4279 G 1.3757 85.2745 83.0000 26.7604 51 8.0582389831543 61.988264132327 43.9111 41.0000 13.9922 186 0.4279
1014 3224.7346 31.1663 G 54.8503 3264.7346 3093.0000 2686.0515 98 11.1703834533691 59.5208328334611 43.0824 40.0000 13.0139 188 31.1663
1015 3060.8076 29.5820 G 53.3144 3099.8076 2678.0000 2744.9539 104 11.5072546005249 58.1420460306122 41.7143 39.0000 12.7614 188 29.5820
1017 7.7885 0.0753 L 0.7977 46.7885 44.0000 16.2969 52 8.1368579864502 58.6514104378099 41.9352 39.0000 13.1009 112 0.0753
1018 17.1268 0.1655 G 1.0039 57.1268 53.0000 21.1200 71 9.50789165496826 56.9048103701471 42.0962 40.0000 11.2699 108 0.1655
1019 30.2115 0.2920 G 1.1715 70.2115 67.0000 28.4823 52 8.1368579864502 59.93210700078 42.1173 40.0000 13.2881 185 0.2920
1020 9.3860 0.0907 L 0.8279 50.3860 48.0000 19.8722 57 8.51907634735107 60.8605595461565 42.3500 41.0000 13.2404 104 0.0907
1021 3149.9333 30.4434 G 54.7619 3189.9333 2679.0000 2770.3362 105 11.562445640564 58.2509112176811 41.3278 40.0000 12.1673 186 30.4434
1022 3278.4761 31.6857 G 55.9905 3319.4761 2662.0000 2819.4595 105 11.562445640564 59.2863781455026 42.4568 41.0000 12.1909 168 31.6857
1024 5.3529 0.0517 L 0.7536 43.3529 40.0000 17.7949 51 8.0582389831543 57.5273036970388 41.7255 38.0000 13.0182 106 0.0517

Total number of rows: 36227

Table truncated, full table size 4575 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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