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Sample GSM258123 Query DataSets for GSM258123
Status Public on Mar 05, 2008
Title F-Genome: slide42
Sample type RNA
 
Channel 1
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 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 = F10C_A10C_A10c5; 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 = A1; 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 = F10C_A10C_A10c5; 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 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 Tissue type = Fiber 10 DPA; Parameter Polyploid level = 2x; Parameter Transgenes = none
Treatment protocol Parameter Genome = F; 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 = F10C_A10C_F10c3; 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 = F10C_A10C_F10c3; 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/2007-10/58014.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 7083 6759 511 485 6572 6274 8451 9080 527 517 7940 8595 0 0 4459 4161 144 192 90 86 80 82 12846 16535 1.047 .955 1.082 1.007 .951 1.458 52 340 .945 .978 80 1780 3130 309 317 174 182 0 10175 730 9445 1.437 13670 12939 .696 1.63 .523 .705
2 1290 544 506 481 784 63 1355 539 516 492 849 58 0 0 568 54 42 64 86 42 78 11 847 907 12.444 .08 .068 .116 .081 5.663 52 340 .101 .275 80 1990 3130 309 317 195 203 0 819 724 95 .121 811 87 8.266 .103 -3.047 -3.281
3 19477 13468 508 482 18969 12986 23551 13802 519 494 23043 13320 0 0 12746 8774 48 70 100 100 100 100 31955 36363 1.461 .685 .578 .732 .709 1.322 52 414 .68 .958 90 2170 3130 308 317 212 221 0 20275 726 19550 1.031 20778 20053 .97 .87 .044 -.201
4 13369 10985 506 481 12863 10504 14871 10659 529 500 14365 10178 0 0 8420 6584 269 131 98 100 96 100 23367 24543 1.225 .817 .709 .918 .833 1.452 52 340 .8 .961 80 2370 3130 309 317 233 241 0 16537 724 15813 1.229 16047 15322 .813 1.067 .298 .093
5 602 771 503 478 99 293 569 501 514 491 66 23 0 0 138 672 39 55 75 33 33 33 392 89 .338 2.96 .348 1.188 1.513 5.454 12 104 6.626 .492 50 2590 3120 309 314 256 261 0 1161 720 441 4.456 754 35 .224 .525 2.156 -.931
6 2676 1906 507 480 2169 1426 1024 622 516 498 517 142 0 0 2360 1794 47 100 100 53 100 47 3595 659 1.521 .657 .275 .293 .429 2.937 120 821 .717 .935 130 2760 3140 307 320 269 282 0 2869 723 2147 .99 936 214 1.01 .413 -.015 -1.274
7 1797 3597 510 482 1287 3115 1823 3680 517 491 1313 3198 0 0 524 1224 35 69 100 100 96 100 4402 4511 .413 2.42 2.436 2.587 2.415 1.452 32 236 2.488 .942 70 2960 3120 308 315 292 299 0 5415 726 4689 3.644 5540 4814 .274 3.667 1.865 1.874
8 645 547 515 478 130 69 616 527 522 492 101 49 0 0 114 78 43 77 87 25 68 9 199 150 1.884 .531 .485 .468 .531 2.716 32 236 1.355 .09 70 3160 3130 309 316 312 319 0 823 720 104 .799 793 74 1.251 .73 -.324 -.453
9 549 480 505 477 44 3 536 469 516 491 31 -8 0 0 54 39 53 82 33 6 13 0 47 23 14.667 .068 null .735 .864 5.01 80 550 .381 0 100 3350 3110 306 316 330 340 -50 723 718 5 .103 706 -12 9.742 null -3.284 null
10 7874 2972 508 478 7366 2494 7964 2936 520 496 7456 2458 0 0 2283 867 50 117 100 100 100 100 9860 9914 2.953 .339 .33 .34 .321 1.29 32 236 .339 .945 70 3550 3120 308 315 351 358 0 4474 720 3755 .51 4420 3700 1.962 .496 -.972 -1.011
11 602 594 500 470 102 124 545 559 514 499 45 89 0 0 245 141 47 93 50 50 8 25 226 134 .823 1.216 1.978 1.911 4.022 7.929 12 68 .232 .021 40 3770 3070 305 309 375 379 0 894 708 187 1.83 842 134 .546 2.977 .872 1.574
12 2285 1706 498 467 1787 1239 2223 1755 507 484 1725 1288 0 0 328 232 41 88 100 100 100 100 3026 3013 1.442 .693 .747 .693 .666 1.176 32 176 .697 .866 60 3930 3110 308 314 390 396 0 2568 703 1865 1.044 2642 1939 .958 1.124 .062 .169
13 1686 1531 504 469 1182 1062 1080 1132 513 477 576 663 0 0 1505 1514 39 58 93 87 87 78 2244 1239 1.113 .898 1.151 .899 .83 1.832 32 176 .975 .954 60 4150 3110 308 314 412 418 0 2305 706 1599 1.353 1704 998 .739 1.733 .436 .793
14 5800 3609 508 480 5292 3129 6080 3738 514 483 5572 3258 0 0 1409 1133 38 32 100 100 100 100 8421 8830 1.691 .591 .585 .572 .572 1.193 32 236 .615 .954 70 4330 3120 308 315 429 436 0 5433 723 4711 .89 5627 4905 1.123 .88 -.168 -.184
15 2822 1906 510 476 2312 1430 2923 1903 519 481 2413 1427 0 0 820 535 45 32 100 100 100 100 3742 3840 1.617 .619 .591 .625 .609 1.223 52 340 .617 .97 80 4520 3110 307 315 448 456 0 2869 717 2153 .931 2865 2148 1.074 .89 -.103 -.168
16 628 500 507 475 121 25 613 503 528 483 106 28 0 0 77 32 163 50 25 15 3 3 146 134 4.84 .207 .264 .272 .331 3.018 32 176 .364 .214 60 4730 3110 308 314 470 476 0 753 715 38 .311 757 42 3.215 .398 -1.685 -1.33
17 1900 1021 497 469 1403 552 1938 1036 510 477 1441 567 0 0 455 224 120 48 100 98 98 96 1955 2008 2.542 .393 .393 .375 .384 1.411 52 340 .39 .883 80 4910 3100 306 314 487 495 0 1537 706 831 .592 1560 854 1.688 .592 -.756 -.755
18 9080 6402 501 473 8579 5929 10058 6161 515 497 9557 5688 0 0 6140 4536 58 136 100 100 100 90 14508 15245 1.447 .691 .595 .713 .68 1.357 52 340 .706 .966 80 5110 3100 306 314 507 515 0 9638 712 8926 1.04 9275 8563 .961 .896 .057 -.158
19 4517 1991 503 474 4014 1517 4683 2108 513 489 4180 1634 0 0 1256 457 55 106 100 100 100 100 5531 5814 2.646 .378 .391 .382 .386 1.227 52 420 .371 .954 90 5300 3100 305 314 525 534 0 2997 714 2284 .569 3173 2460 1.758 .588 -.814 -.765
20 23397 27375 506 480 22891 26895 30039 33130 518 503 29533 32650 0 0 14865 18004 57 180 100 96 100 88 49786 62183 .851 1.175 1.106 1.17 1.162 1.217 52 420 1.191 .985 90 5490 3100 305 314 544 553 0 41212 723 40489 1.769 49876 49153 .565 1.664 .823 .735

Total number of rows: 24288

Table truncated, full table size 5421 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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