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Sample GSM115003 Query DataSets for GSM115003
Status Public on Feb 15, 2007
Title Endometrium 4 WG
Sample type RNA
 
Source name endometrium
Organism Homo sapiens
Characteristics Human, female, of reproductive age, endometrial biopsy of eutopic endometrium, early secretory 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 8304.8203 97.1956 G 120.0490 8351.8203 3917.0000 8885.6250 50 7.97884559631348 69.5701104139489 49.6111 47.0000 15.0467 74 GE200017
1002 528.4074 6.1842 I 7.1986 577.4074 700.0000 333.2901 27 5.86323022842407 80.2111412909378 49.0870 49.0000 20.8074 23 GE766244
1003 11.6429 0.1363 L 0.8125 56.6429 48.0000 19.2079 14 4.222008228302 69.7158858278908 49.0000 45.0000 16.4773 20 GE766859
1004 5.6923 0.0666 L 0.7885 54.6923 54.0000 16.6520 13 4.0684289932251 69.3642032387033 50.5313 49.0000 13.5761 32 GE519376
1005 5.5000 0.0644 L 0.7387 55.5000 55.0000 17.2285 14 4.222008228302 75.1337010179982 48.8438 50.0000 16.7558 32 GE519777
1006 12.2667 0.1436 L 0.8666 62.2667 58.0000 16.3522 15 4.37019395828247 71.8531552420596 48.4688 50.0000 14.5688 32 GE895719
1007 7.8571 0.0920 L 0.7735 54.8571 51.0000 23.6790 14 4.222008228302 70.9203573796729 50.4063 47.0000 15.9469 32 GE896168
1008 9276.4541 108.5671 I 127.9017 9326.4541 4443.0000 9478.3994 55 8.36828422546387 72.918933528446 52.1176 50.0000 15.2793 70 GE200018
1009 164.2174 1.9219 I 2.5419 229.2174 206.0000 82.7784 23 5.4115161895752 90.1766651718629 63.8846 65.0000 16.7844 26 GE768684
1010 341.2692 3.9940 I 5.9330 388.2692 408.0000 230.0626 26 5.75362730026245 65.441956781893 47.6429 47.0000 12.2946 28 GE769330
1011 45.5652 0.5333 G 1.3648 89.5652 93.0000 20.6310 23 5.4115161895752 65.6241162293079 47.1000 44.0000 14.4161 30 GE521062
1012 175.9565 2.0593 I 2.5825 229.9565 247.0000 82.2623 23 5.4115161895752 89.0452891211793 52.8710 54.0000 23.3635 31 GE521431
1013 26.5152 0.3103 G 1.0387 70.5152 70.0000 22.8077 33 6.48204469680786 67.8896603014799 48.0545 44.0000 15.9264 57 GE897528
1014 49.5238 0.5796 G 1.3749 97.5238 86.0000 31.6222 21 5.17088317871094 70.9295629038178 50.9355 48.0000 15.2864 31 GE897998
1015 9779.9189 114.4594 I 109.0001 9840.9189 7568.0000 8839.0703 37 6.86366271972656 90.2835968552358 61.4688 61.0000 19.5224 32 GE200019
1016 27.8000 0.3254 G 1.0380 81.8000 83.0000 17.9748 15 4.37019395828247 78.8047472468107 57.0769 54.0000 16.5365 26 GE766257
1017 4.4615 0.0522 L 0.7708 58.4615 58.0000 15.3453 13 4.0684289932251 75.8485864622884 53.0323 54.0000 14.5657 31 GE766861
1018 10.8000 0.1264 L 0.8213 60.8000 53.0000 21.4544 15 4.37019395828247 74.0277714075379 51.9688 50.0000 16.0185 32 GE519380
1019 11.1429 0.1304 L 0.7657 60.1429 65.0000 14.5987 14 4.222008228302 78.5448546811161 53.1034 49.0000 19.6966 29 GE519781
1020 38.4737 0.4503 G 1.1963 84.4737 82.0000 15.7492 19 4.91849088668823 70.6116563694583 50.6875 46.0000 16.4078 32 GE895725

Total number of rows: 54359

Table truncated, full table size 6869 Kbytes.




Supplementary data files not provided

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