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Sample GSM115007 Query DataSets for GSM115007
Status Public on Feb 15, 2007
Title Endometrium 6B WG
Sample type RNA
 
Source name endometrium
Organism Homo sapiens
Characteristics Human, female, of reproductive age, endometrial biopsy of eutopic endometrium, proliferative phase
Extracted molecule total RNA
Extraction protocol The eutopic and ectopic endometrial samples were placed in RNAlater (Ambion) in the surgical suite. The endometrial samples were homogenized in TRI reagent (MRC) using a Polytron (Brinkmann). 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 was evaluated with the RNA 6000 NanoLabChip in an Agilent Bioanalyzer.
Label Alexa-647
Label protocol see CodeLink application notes and manuals
 
Hybridization protocol see CodeLink application notes and manuals
Scan protocol see CodeLink application notes and manuals
Description Each patient served as her own control; the eutopic endometrial biopsies were obtained from the patients at the same surgery in which the endometriotic explants were excised. IRB approval and informed consent were obtained for all sample collection.
Data processing global median normalization, CodeLink Expression Analysis 4.1.0.4163
 
Submission date Jun 16, 2006
Last update date Feb 12, 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 GPL2895
Series (1)
GSE5108 Whole human genome DNA microarray analysis of gene expression in ectopic vs. eutopic endometrium

Data table header descriptions
ID_REF #Raw_intensity = Raw signal intensity value
Raw_intensity
VALUE Median normalized signal intensity value
Quality_flag CodeLink quality flag
Signal_strength Signal strength
Spot_mean Spot median
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
Probe_name CodeLink probe name

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 Probe_name
1001 8296.8633 118.2732 G 125.1141 8343.8633 2212.0000 8896.1143 44 7.48482084274292 66.6900532046259 48.8485 47.0000 13.1267 68 GE200017
1002 378.4400 5.3947 I 6.1504 428.4400 443.0000 247.4719 25 5.64189577102661 69.6602924215815 52.1290 50.0000 13.1069 31 GE766244
1003 16.5294 0.2356 L 0.9697 59.5294 58.0000 17.3853 17 4.65242671966553 61.3900620706446 45.9375 43.0000 12.2600 32 GE766859
1004 12.4286 0.1772 L 0.8263 55.4286 64.0000 16.6163 14 4.222008228302 67.0797922665184 45.8621 43.0000 16.0532 29 GE519376
1005 18.2857 0.2607 G 1.0265 59.2857 63.0000 18.3242 14 4.222008228302 57.7579243946345 41.2500 41.0000 11.1720 32 GE519777
1006 16.3750 0.2334 L 0.9070 64.3750 72.0000 23.8141 16 4.51351690292358 70.9785051506791 49.1250 48.0000 15.3190 32 GE895719
1007 3.8571 0.0550 L 0.7484 52.8571 52.0000 20.2232 14 4.222008228302 70.6227415724753 48.8750 49.0000 14.4152 32 GE896168
1008 13239.9658 188.7379 C 91.5458 13286.9658 16984.0000 9395.5576 29 6.07650756835938 145.140153508359 65.9333 47.0000 65.4268 30 GE200018
1009 234.9091 3.3487 I 3.8208 285.9091 281.0000 89.5265 22 5.29256725311279 74.8302036083047 50.3846 51.0000 15.8868 26 GE768684
1010 264.1818 3.7660 I 4.3135 319.1818 347.0000 96.2641 22 5.29256725311279 73.9967145627118 53.3333 55.0000 12.6645 24 GE769330
1011 42.0000 0.5987 G 1.2292 84.0000 78.0000 30.0644 15 4.37019395828247 68.338607478925 45.7778 42.0000 17.5591 27 GE521062
1012 51.0000 0.7270 G 1.5744 97.0000 97.0000 34.7150 23 5.4115161895752 61.60883847353 47.2963 46.0000 10.4059 27 GE521431
1013 9.3226 0.1329 L 0.7826 53.3226 49.0000 14.2476 31 6.2825493812561 68.1350288456647 48.8873 44.0000 16.0900 73 GE897528
1014 20.2857 0.2892 L 0.9337 63.2857 60.0000 21.7072 14 4.222008228302 67.7796345883594 47.6875 43.0000 16.5198 32 GE897998
1015 9166.0859 130.6641 I 135.4057 9213.0859 6565.0000 8760.4785 35 6.67558097839355 68.0406213875992 48.7500 47.0000 14.0271 28 GE200019
1016 23.8333 0.3397 L 0.9739 68.8333 72.0000 21.7773 18 4.78730726242065 70.6782992556154 49.3333 45.0000 17.1189 24 GE766257
1017 8.1000 0.1155 L 0.7872 56.1000 55.0000 15.5978 30 6.18038702011108 71.2632316572297 49.9841 48.0000 15.5088 65 GE766861
1018 7.4615 0.1064 L 0.7352 56.4615 55.0000 15.7559 13 4.0684289932251 76.7974700148801 52.6250 49.0000 18.5316 32 GE519380
1019 7.1429 0.1018 L 0.7551 53.1429 50.0000 17.0707 14 4.222008228302 70.37745014732 49.4667 46.0000 16.2516 30 GE519781
1020 19.1429 0.2729 L 0.9191 67.1429 63.0000 24.1834 14 4.222008228302 73.0537454343447 50.4000 48.0000 16.7025 30 GE895725

Total number of rows: 54359

Table truncated, full table size 6856 Kbytes.




Supplementary data files not provided

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