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Sample GSM258127 Query DataSets for GSM258127
Status Public on Mar 05, 2008
Title F-Genome: slide45
Sample type RNA
 
Channel 1
Source name Fiber at 5 DPA derived from F-genome
Organism Gossypium longicalyx
Characteristics Fiber at 5 DPA derived from F-genome
Parameter Species = Gossypium longicalyx; Parameter Genome = F; Parameter Polyploid level = 2x; Parameter Tissue type = Fiber 5 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 = F5C_A5C_F5c5; 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 = 3/20/2007; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F5C_A5C_F5c5; Parameter Date performed = 3/22/2007; 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 5 DPA derived from A-genome
Organism Gossypium herbaceum
Characteristics Fiber at 5 DPA derived from A-genome
Parameter Species = Gossypium herbaceum; Parameter Genome = A1; Parameter Tissue type = Fiber 5 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 = F5C_A5C_A5c3; 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 = 3/20/2007; 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 = 3/22/2007; Parameter Tube label = F5C_A5C_A5c3; 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 = 3/23/2007; 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 = 3/23/2007; 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/2007-10/58017.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 13164 8804 509 469 12655 8335 14556 9642 512 476 14047 9173 0 0 3803 2354 30 43 100 100 100 100 20990 23220 1.518 .659 .653 .668 .653 1.118 32 236 .651 .989 70 1760 2930 289 296 172 179 0 11681 622 11058 .874 12793 12170 1.144 .866 -.195 -.207
2 713 1335 495 468 218 867 688 1394 499 484 193 926 0 0 135 545 29 103 96 96 90 90 1085 1119 .251 3.977 4.798 3.859 3.87 1.541 32 236 4.184 .393 70 1950 2920 288 295 191 198 0 1771 621 1150 5.277 1849 1229 .19 6.366 2.4 2.67
3 24905 20212 509 487 24396 19725 26298 21298 516 497 25789 20811 0 0 16070 13309 56 73 100 100 100 100 44121 46600 1.237 .809 .807 .844 .823 1.322 52 340 .815 .993 80 2150 2930 289 297 211 219 0 26816 646 26170 1.073 28257 27611 .932 1.071 .101 .098
4 17169 13140 504 481 16665 12659 19133 14767 505 492 18629 14286 0 0 6063 4551 29 61 100 100 100 100 29324 32915 1.316 .76 .767 .762 .792 1.162 32 236 .752 .98 70 2330 2930 289 296 229 236 0 17434 638 16795 1.008 19592 18954 .992 1.017 .011 .025
5 695 513 491 474 204 39 690 521 498 483 199 47 0 0 114 42 34 49 100 40 87 12 243 246 5.231 .191 .236 .271 .284 2.176 32 176 1.344 .062 60 2540 2940 291 297 251 257 0 681 629 52 .254 691 62 3.943 .313 -1.979 -1.674
6 2632 3051 500 478 2132 2573 2668 2936 507 488 2168 2458 0 0 1533 2226 46 59 100 83 100 76 4705 4626 .829 1.207 1.134 .611 1.119 3.246 80 622 1.328 .965 110 2740 2940 288 299 268 279 0 4048 634 3414 1.601 3895 3261 .625 1.504 .679 .589
7 1389 1105 498 476 891 629 1470 1085 507 484 972 609 0 0 343 365 40 35 100 100 96 96 1520 1581 1.417 .706 .627 .687 .706 1.342 32 236 .75 .805 70 2930 2930 289 296 289 296 0 1466 632 835 .937 1440 808 1.068 .831 -.094 -.267
8 548 502 496 482 52 20 532 484 507 514 36 2 0 0 62 59 57 251 31 0 11 0 72 38 2.6 .385 .056 .617 .572 6.557 80 542 2.99 .116 100 3120 2920 287 297 307 317 -50 666 639 27 .51 642 3 1.96 .074 -.971 -3.762
9 483 508 474 469 9 39 477 497 479 490 3 28 0 0 36 96 34 209 17 2 7 1 48 31 .231 4.333 9.333 2.294 1.875 4.099 80 540 6.839 .052 100 3320 2920 287 297 327 337 -50 674 622 52 5.749 659 37 .174 12.383 2.523 3.63
10 1348 1690 474 461 874 1229 1314 1684 481 467 840 1223 0 0 231 329 30 33 100 100 100 100 2103 2063 .711 1.406 1.456 1.404 1.428 1.387 32 176 1.453 .893 60 3520 2940 291 297 349 355 0 2242 612 1631 1.866 2234 1623 .536 1.932 .9 .95
11 514 500 473 461 41 39 494 472 481 474 21 11 0 0 103 118 43 77 27 10 8 3 80 32 1.051 .951 .524 .781 1.061 4.797 80 550 .863 .046 100 3710 2920 287 297 366 376 -50 663 612 52 1.262 626 15 .792 .695 .336 -.525
12 3576 3041 471 455 3105 2586 3594 3126 474 461 3123 2671 0 0 775 594 26 37 100 100 100 100 5691 5794 1.201 .833 .855 .839 .826 1.2 32 236 .806 .954 70 3910 2930 289 296 387 394 0 4035 604 3431 1.105 4147 3544 .905 1.135 .144 .182
13 517 486 465 456 52 30 491 472 492 476 26 16 0 0 89 67 326 140 2 5 0 1 82 42 1.733 .577 .615 .849 .642 5.444 80 556 .352 .862 100 4100 2920 287 297 405 415 -50 645 605 40 .765 626 21 1.306 .816 -.386 -.293
14 8705 10655 469 461 8236 10194 8822 11157 474 467 8353 10696 0 0 2497 3184 31 36 100 100 100 100 18430 19049 .808 1.238 1.28 1.248 1.226 1.181 32 236 1.231 .974 70 4300 2930 289 296 426 433 0 14137 612 13525 1.642 14803 14191 .609 1.699 .716 .765
15 4231 3160 475 463 3756 2697 4504 3522 478 471 4029 3059 0 0 1597 1148 26 40 100 100 100 98 6453 7088 1.393 .718 .759 .698 .73 1.222 52 340 .712 .969 80 4490 2930 289 297 445 453 0 4193 614 3578 .953 4673 4059 1.05 1.007 -.07 .011
16 534 485 488 476 46 9 518 472 494 489 30 -4 0 0 67 79 36 70 47 6 28 1 55 26 5.111 .196 null .552 .539 4.198 80 541 2.61 .038 100 4680 2920 287 297 463 473 -50 643 632 12 .26 626 -5 3.852 null -1.946 null
17 1086 1809 479 465 607 1344 1124 1784 483 470 645 1319 0 0 201 354 29 42 100 100 100 100 1951 1964 .452 2.214 2.045 2.288 2.219 1.354 52 340 2.21 .918 80 4880 2920 288 296 484 492 0 2400 617 1783 2.938 2367 1750 .34 2.713 1.555 1.44
18 12612 13676 473 464 12139 13212 13172 14115 505 469 12699 13651 0 0 2836 3382 289 33 100 100 100 100 25351 26350 .919 1.088 1.075 1.082 1.069 1.102 32 236 1.096 .989 70 5080 2930 289 296 504 511 0 18145 616 17529 1.444 18727 18112 .693 1.426 .53 .512
19 5749 4199 480 461 5269 3738 5830 4206 543 477 5350 3745 0 0 1395 1051 551 81 100 100 98 100 9007 9095 1.41 .709 .7 .701 .705 1.164 52 334 .71 .976 80 5270 2930 289 297 523 531 0 5571 612 4959 .941 5580 4969 1.062 .929 -.087 -.107
20 28799 17675 510 469 28289 17206 39600 22243 521 476 39090 21774 0 0 17756 10824 63 62 100 100 100 100 45495 60864 1.644 .608 .557 .607 .613 1.232 52 340 .608 .993 80 5470 2930 289 297 543 551 0 23450 622 22828 .807 29511 28889 1.239 .739 -.309 -.436

Total number of rows: 24288

Table truncated, full table size 5424 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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