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Sample GSM115000 Query DataSets for GSM115000
Status Public on Feb 15, 2007
Title Endometriosis 2 WG
Sample type RNA
 
Source name endometriosis
Organism Homo sapiens
Characteristics Human, female, of reproductive age, severe endometriosis, endometrioma
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 8212.5625 129.5584 G 116.1104 8262.5625 2981.0000 8937.6084 48 7.81764030456543 71.1612674858322 50.2432 50.0000 14.1075 76 GE200017
1002 587.3913 9.2665 I 7.2350 641.3913 676.0000 256.0113 23 5.4115161895752 88.6509225404518 56.0400 54.0000 23.1006 25 GE766244
1003 -1.0769 -0.0170 L 0.6874 50.9231 50.0000 11.9194 13 4.0684289932251 74.079544160809 52.8148 52.0000 14.7197 27 GE766859
1004 3.3333 0.0526 L 0.7385 53.3333 44.0000 20.4798 15 4.37019395828247 72.2214261874907 53.9643 50.0000 14.8143 28 GE519376
1005 -1.9333 -0.0305 L 0.6842 55.0667 52.0000 16.9311 30 6.18038702011108 80.4820483192655 54.6351 57.0000 15.6547 76 GE519777
1006 11.2857 0.1780 L 0.7986 64.2857 55.0000 25.5327 14 4.222008228302 80.4948150273267 52.6250 53.0000 18.3299 32 GE895719
1007 19.6154 0.3094 L 0.9341 68.6154 68.0000 23.7634 13 4.0684289932251 73.453079238389 50.8438 49.0000 16.3020 32 GE896168
1008 9374.0596 147.8818 I 137.0392 9423.0596 3453.0000 9639.1045 50 7.97884559631348 68.7618048684567 50.5645 49.0000 13.1745 64 GE200018
1009 61.7500 0.9741 I 1.5655 112.7500 110.0000 35.3537 20 5.04626512527466 72.0236423732382 54.2800 51.0000 14.0158 25 GE768684
1010 264.3750 4.1707 I 4.6617 310.3750 310.0000 142.9801 24 5.52790641784668 66.5803910617668 46.4333 46.0000 13.7203 30 GE769330
1011 34.5000 0.5443 G 1.1928 81.5000 85.0000 22.3075 16 4.51351690292358 68.3255995703413 48.5000 47.0000 14.2171 32 GE521062
1012 77.5556 1.2235 I 1.7168 127.5556 127.0000 47.2890 18 4.78730726242065 74.2970713368519 53.4516 50.0000 16.1980 31 GE521431
1013 28.8824 0.4556 G 1.0781 77.8824 74.0000 31.4416 17 4.65242671966553 72.2426918254488 51.6333 49.0000 15.4951 30 GE897528
1014 18.1333 0.2861 L 0.8999 64.1333 65.0000 16.0701 15 4.37019395828247 71.2643655504963 48.8387 46.0000 16.8429 31 GE897998
1015 8215.0000 129.5969 G 112.2730 8265.0000 2715.0000 9013.6719 43 7.3992772102356 73.6152090746261 52.6866 50.0000 15.7435 69 GE200019
1016 1444.3600 22.7857 I 18.1252 1495.3600 1879.0000 1030.3982 25 5.64189577102661 82.5015954181267 54.2903 51.0000 21.0011 31 GE766257
1017 14.4667 0.2282 L 0.8802 63.4667 58.0000 17.8283 15 4.37019395828247 72.1063268241792 52.6923 49.0000 15.4042 26 GE766861
1018 5.2424 0.0827 L 0.7639 55.2424 49.0000 19.7914 33 6.48204469680786 72.3186974467471 51.1408 50.0000 14.8791 73 GE519380
1019 -1.2308 -0.0194 L 0.6650 50.7692 47.0000 12.1538 13 4.0684289932251 76.3465449089237 52.8064 52.0000 16.2310 31 GE519781
1020 12.2000 0.1925 L 0.7779 70.2000 69.0000 19.3673 15 4.37019395828247 90.2434441816619 59.7333 58.0000 21.4956 30 GE895725

Total number of rows: 54359

Table truncated, full table size 6847 Kbytes.




Supplementary data files not provided

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