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Sample GSM115009 Query DataSets for GSM115009
Status Public on Feb 15, 2007
Title Endometrium 7 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 7309.4917 147.5473 G 82.1614 7360.4917 8454.0000 5665.5400 126 12.6660251617432 89.5857880207885 55.2966 51.0000 25.7239 122 GE200017
1002 156.5797 3.1607 G 2.4515 205.5797 193.0000 71.6290 69 9.37302112579346 83.8577922991722 54.3901 49.0000 23.2385 188 GE766244
1003 2.8400 0.0573 L 0.6573 52.8400 45.0000 28.4706 50 7.97884559631348 80.3856240442676 54.4750 50.0000 20.2571 124 GE766859
1004 7.6667 0.1548 L 0.6379 61.6667 55.0000 31.4805 30 6.18038702011108 96.6783010739043 60.8936 54.0000 28.4522 145 GE519376
1005 16.3636 0.3303 L 0.7126 85.3636 83.0000 33.1527 55 8.36828422546387 119.796986129652 76.7200 69.0000 33.8647 77 GE519777
1006 29.3889 0.5932 L 0.8624 98.3889 100.0000 34.9883 36 6.7702751159668 114.092826014983 75.9441 69.0000 30.0619 147 GE895719
1007 31.1026 0.6278 L 0.8835 99.1026 92.0000 43.0883 39 7.04672574996948 112.164697148959 73.2278 68.0000 29.4431 186 GE896168
1008 6921.2573 139.7105 G 82.0855 6971.2573 8897.0000 5289.5479 138 13.2554540634155 84.9267393343468 54.9310 50.0000 23.2845 120 GE200018
1009 160.9744 3.2494 G 2.4688 213.9744 207.0000 72.4240 78 9.96557521820068 86.6727253412447 55.0618 53.0000 22.4485 184 GE768684
1010 90.5692 1.8282 G 1.7079 142.5692 128.0000 55.2090 65 9.09728336334229 83.4759344821781 54.3600 52.0000 20.9840 129 GE769330
1011 21.6792 0.4376 L 0.7509 84.6792 83.0000 40.2107 53 8.21472454071045 112.763752141384 73.0750 63.0000 33.1758 124 GE521062
1012 30.4737 0.6151 L 0.9090 95.4737 101.0000 36.4993 38 6.95579624176025 105.028915787313 68.7348 65.0000 26.6859 187 GE521431
1013 15.6563 0.3160 L 0.7465 63.6563 52.0000 28.9910 32 6.38307666778564 85.2757098592798 55.2418 48.0000 24.8505 188 GE897528
1014 7.6000 0.1534 L 0.6748 62.6000 60.0000 27.4634 30 6.18038702011108 92.7662125665028 57.3077 55.0000 25.1775 188 GE897998
1015 6676.2778 134.7654 G 75.4529 6731.2778 8664.0000 4946.6094 110 11.8345403671265 89.2116742974551 57.6483 55.0000 22.8078 188 GE200019
1016 41.2750 0.8332 G 1.0773 92.2750 89.0000 39.8378 40 7.13649654388428 85.6554145324062 53.5952 51.0000 23.1036 174 GE766257
1017 12.0606 0.2435 L 0.7450 63.0606 56.0000 30.4829 33 6.48204469680786 84.6445418913827 54.5183 51.0000 22.4297 170 GE766861
1018 6.9670 0.1406 L 0.6594 54.9670 48.0000 27.8206 91 10.7640514373779 83.3547062192321 53.7185 48.0000 23.5698 139 GE519380
1019 8.0000 0.1615 L 0.7049 59.0000 51.0000 25.2265 32 6.38307666778564 83.7011218007665 52.9392 51.0000 21.8007 187 GE519781
1020 22.2239 0.4486 L 0.8214 75.2239 67.0000 39.4177 67 9.23618125915527 91.5812701106612 56.4333 53.0000 25.7209 124 GE895725

Total number of rows: 54359

Table truncated, full table size 6892 Kbytes.




Supplementary data files not provided

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