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Sample GSM258115 Query DataSets for GSM258115
Status Public on Mar 05, 2008
Title F-Genome: slide14
Sample type RNA
 
Channel 1
Source name Fiber at 10 DPA derived from F-genome
Organism Gossypium longicalyx
Characteristics Fiber at 10 DPA derived from F-genome
Parameter Species = Gossypium longicalyx; Parameter Genome = F; Parameter Polyploid level = 2x; Parameter Tissue type = Fiber 10 DPA; Parameter Transgenes = none
Extracted molecule total RNA
Extraction protocol Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F10A_A10A_F10c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran
Label Cy3
Label protocol Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = F; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 12/29/2006; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F10A_A10A_F10c5; Parameter Date performed = 1/2/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran
 
Channel 2
Source name Fiber at 10 DPA derived from A-genome
Organism Gossypium herbaceum
Characteristics Fiber at 10 DPA derived from A-genome
Parameter Species = Gossypium herbaceum; Parameter Genome = A1; Parameter Tissue type = Fiber 10 DPA; Parameter Polyploid level = 2x; Parameter Transgenes = none
Treatment protocol Parameter Genome = A1; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Extracted molecule total RNA
Extraction protocol Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F10A_A10A_A10c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA
Label Cy5
Label protocol Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 12/29/2006; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 12/22/2006; Parameter Tube label = F10A_A10A_A10c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran
 
 
Hybridization protocol not provided
Scan protocol Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = Gal file; Software: type: feature extraction
Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Applied Precision; Parameter Scan Temperature = RT; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 1/3/2007; Parameter Pixel Size = 10 um; Parameter Scanner Model = arrayWoRx Biochip Reader; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Software Suite
Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Temperature = RT; Parameter Scanner Make = Applied Precision; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 1/3/2007; Parameter Pixel Size = 10 um; Parameter Scanner Model = arrayWoRx Biochip Reader; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Software Suite
Description Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/57986.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Jan 22, 2008
Last update date Mar 04, 2008
Contact name Alan R Gingle
E-mail(s) agingle@uga.edu
Organization name University of Georgia
Department Center for Applied Genetics Technologies
Lab Gingle lab
Street address 111 Riverbend Rd.
City Athens
State/province GA
ZIP/Postal code 30602
Country USA
 
Platform ID GPL4808
Series (1)
GSE10228 The evolution of spinable cotton fiber entailed prolonged development and a novel metabolism

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
LOG_RAT2N_MEAN Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2
VALUE Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN LOG_RAT2N_MEAN VALUE
1 9648 8896 575 485 9073 8411 11263 10194 586 491 10688 9709 0 0 3404 3301 50 33 100 100 100 100 17484 20397 1.079 .927 .908 .908 .937 1.142 32 236 .935 .99 70 1740 2970 293 300 170 177 0 7185 392 6793 .749 8233 7842 1.336 .734 -.417 -.447
2 702 1683 554 475 148 1208 681 1464 560 481 127 989 0 0 124 581 46 32 81 100 59 100 1356 1116 .123 8.162 7.787 11.633 8.603 2.538 32 176 7.574 .634 60 1950 2970 294 300 192 198 0 1359 384 976 6.592 1182 799 .152 6.29 2.721 2.653
3 21674 28010 562 495 21112 27515 23910 30781 571 500 23348 30286 0 0 6292 7974 48 37 100 100 100 100 48627 53634 .767 1.303 1.297 1.311 1.323 1.087 32 236 1.298 .992 70 2130 2970 293 300 209 216 0 22623 400 22223 1.053 24861 24461 .95 1.048 .074 .067
4 22780 19518 561 497 22219 19021 24802 21659 572 503 24241 21162 0 0 7465 6358 51 37 100 100 100 100 41240 45403 1.168 .856 .873 .862 .852 1.139 32 236 .823 .914 70 2330 2980 294 301 229 236 0 15764 401 15363 .691 17493 17092 1.446 .705 -.532 -.504
5 1229 586 578 487 651 99 701 574 606 496 123 87 0 0 2901 147 275 35 9 81 9 62 750 210 6.576 .152 .707 .651 .643 2.946 32 176 .078 .869 60 2510 2970 294 300 248 254 0 473 393 80 .123 464 70 8.142 .571 -3.025 -.808
6 4061 7296 600 489 3461 6807 4689 8874 609 496 4089 8385 0 0 1728 3585 58 34 100 100 100 100 10268 12474 .508 1.967 2.051 1.69 1.934 1.522 52 340 2.041 .979 80 2710 2990 295 303 267 275 0 5893 395 5498 1.588 7167 6772 .63 1.656 .668 .728
7 4071 1991 586 490 3485 1501 4511 2215 595 492 3925 1725 0 0 1356 587 52 26 100 100 100 100 4986 5650 2.322 .431 .439 .436 .433 1.167 32 236 .428 .981 70 2920 2970 293 300 288 295 0 1608 396 1212 .348 1789 1393 2.875 .355 -1.523 -1.494
8 614 501 586 494 28 7 604 495 597 499 18 1 0 0 55 39 58 37 27 21 7 6 35 19 4 .25 .056 .745 .725 3.873 80 556 .339 .102 100 3110 2970 292 302 306 316 -50 405 399 6 .202 400 1 4.953 .045 -2.308 -4.478
9 564 746 560 485 4 261 574 726 571 503 14 241 0 0 36 88 59 73 0 100 0 100 265 255 .015 65.25 17.214 11.209 12.895 2.053 12 68 -162.002 .001 40 3320 2980 296 300 330 334 0 603 392 211 52.7 586 195 .019 13.903 5.72 3.797
10 4377 6070 566 482 3811 5588 4991 7179 576 488 4425 6697 0 0 1548 2271 54 41 100 100 100 100 9399 11122 .682 1.466 1.513 1.526 1.519 1.267 32 176 1.475 .981 60 3510 2990 296 302 348 354 0 4903 389 4513 1.184 5798 5409 .844 1.222 .244 .29
11 571 472 555 478 16 -6 563 468 568 482 8 -10 0 0 39 30 59 33 15 12 0 1 10 -2 null null null .985 .861 4.247 80 550 .101 .008 100 3690 2970 292 302 364 374 -50 381 386 -5 null 378 -8 null null null null
12 2130 2492 558 476 1572 2016 2261 2692 567 481 1703 2216 0 0 558 651 49 39 100 100 100 100 3588 3919 .78 1.282 1.301 1.312 1.305 1.262 32 176 1.281 .937 60 3890 2970 294 300 386 392 0 2013 384 1628 1.036 2174 1790 .965 1.051 .051 .072
13 542 472 554 478 -12 -6 535 468 561 484 -19 -10 0 0 38 29 50 39 7 8 1 1 -18 -29 null null null .747 .719 3.263 80 556 .255 .049 100 4080 2970 292 302 403 413 -50 381 386 -5 null 378 -8 null null null null
14 5428 14628 554 492 4874 14136 5838 15474 568 498 5284 14982 0 0 1323 3376 55 37 100 100 100 100 19010 20266 .345 2.9 2.835 2.938 2.923 1.138 32 176 2.896 .979 60 4280 2970 294 300 425 431 0 11815 397 11417 2.342 12498 12100 .427 2.29 1.228 1.195
15 3071 3442 560 487 2511 2955 3295 3737 568 496 2735 3250 0 0 826 1002 50 45 100 100 100 100 5466 5985 .85 1.177 1.188 1.173 1.176 1.198 52 340 1.182 .98 80 4480 2980 294 302 444 452 0 2780 393 2387 .95 3018 2625 1.052 .96 -.073 -.059
16 577 528 558 485 19 43 572 527 570 492 14 42 0 0 38 56 65 40 15 51 0 28 62 56 .442 2.263 3 1.694 1.642 2.762 80 533 .712 .103 100 4670 2970 292 302 462 472 -50 426 392 35 1.828 426 34 .547 2.423 .87 1.277
17 1107 1464 537 475 570 989 1114 1462 545 480 577 987 0 0 183 238 46 48 100 100 100 100 1559 1564 .576 1.735 1.711 1.793 1.64 1.395 32 236 1.724 .853 70 4870 2970 293 300 483 490 0 1182 384 799 1.401 1181 797 .714 1.382 .487 .466
18 9789 25037 528 485 9261 24552 11014 27329 533 485 10486 26844 0 0 2492 6161 39 32 100 100 100 100 33813 37330 .377 2.651 2.56 2.672 2.63 1.106 32 176 2.647 .992 60 5060 2970 294 300 503 509 0 20222 392 19830 2.141 22073 21681 .467 2.068 1.098 1.048
19 3344 4089 536 475 2808 3614 3496 4373 559 487 2960 3898 0 0 874 1178 85 60 100 100 100 100 6422 6858 .777 1.287 1.317 1.267 1.247 1.158 52 334 1.298 .984 80 5260 2980 294 302 522 530 0 3303 384 2919 1.039 3532 3148 .962 1.064 .056 .089
20 26681 15064 555 472 26126 14592 5514 1977 575 479 4959 1505 31 0 29837 17464 139 41 96 96 85 87 40718 6464 1.79 .559 .303 .45 .493 1.855 80 617 .546 .917 110 5460 2970 291 302 540 551 0 12167 381 11785 .451 1597 1216 2.217 .245 -1.148 -2.028

Total number of rows: 24288

Table truncated, full table size 5425 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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