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Sample GSM498989 Query DataSets for GSM498989
Status Public on Jan 21, 2010
Title AD4_REP2_LEAF
Sample type RNA
 
Channel 1
Source name AD4 no-salt leaf
Organism Gossypium mustelinum
Characteristics treatment: no-salt
name: 15-c
genome: ad4
polyploid level: 4x
tissue type: leaf
Treatment protocol BYU growth chamber
Extracted molecule total RNA
Extraction protocol Date performed = May-07; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD4 no-salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 2 plants"
Label Cy3
Label protocol Approx RNA yield = 38 ug; Type of in-vitro transcription = Epicentre; Date performed = Sep-07; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD4 no-salt leaf; Date performed = 9/5/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura
 
Channel 2
Source name AD4 salt leaf
Organism Gossypium mustelinum
Characteristics treatment: salt
name: 15-c
genome: ad4
tissue type: leaf
polyploid level: 4x
Treatment protocol BYU growth chamber
Extracted molecule total RNA
Extraction protocol Date performed = May-07; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD4 salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 2 plants"; Name = Rozaura; Extracted molecule = RNA
Label Cy5
Label protocol Approx RNA yield = 6.3 ug; Date performed = Sep-07; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 9/5/2007; Tube label = AD4 salt leaf; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura
 
 
Hybridization protocol not provided
Scan protocol Scanner Make = Agilent; Scan Temperature = RT; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 9/12/2007
Scanner Make = Agilent; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 9/12/2007
Description Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58087.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 20, 2010
Last update date Jan 20, 2010
Contact name Alan R Gingle
E-mail(s) [email protected]
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)
GSE19966 Transcriptional responses of allotetraploid cotton species to salt stress

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 2239 4526 108 81 2131 4445 2351 4830 117 86 2243 4749 0 0 573 1097 120 62 100 100 100 100 6576 6992 .479 2.086 2.117 2.119 2.127 1.157 120 820 2.08 .984 120 3380 4990 493 505 332 344 100 2115 38 2077 .975 2257 2219 1.026 .989 -.037 -.015
2 1972 1576 104 81 1868 1495 1835 1491 112 87 1731 1410 0 0 758 593 50 36 100 100 100 100 3363 3141 1.249 .8 .815 .804 .805 1.177 120 820 .796 .973 120 3770 4970 491 503 371 383 100 736 38 699 .374 697 659 2.674 .381 -1.419 -1.394
3 4015 8270 110 83 3905 8187 3916 8688 115 87 3806 8605 0 0 1054 1875 52 29 100 100 100 100 12092 12411 .477 2.097 2.261 2.119 2.11 1.148 120 940 2.082 .979 130 4150 4970 490 503 408 421 100 3864 39 3825 .98 4060 4021 1.021 1.056 -.03 .079
4 430 1148 112 87 318 1061 421 1154 121 91 309 1067 0 0 79 186 52 26 99 100 99 100 1379 1376 .3 3.336 3.453 3.414 3.443 1.285 120 940 3.341 .883 130 4520 4980 491 504 445 458 100 536 41 496 1.559 539 499 .641 1.613 .641 .69
5 578 1513 116 100 462 1413 574 1548 120 102 458 1448 0 0 252 555 36 20 100 100 99 100 1875 1906 .327 3.058 3.162 3.157 3.125 1.298 120 820 2.9 .913 120 4900 4980 492 504 484 496 100 707 47 660 1.429 723 677 .7 1.477 .515 .563
6 580 4506 119 119 461 4387 627 5137 139 140 508 5018 0 0 283 2100 148 105 79 100 72 97 4848 5526 .105 9.516 9.878 11.289 10.021 1.948 208 1512 9.117 .899 160 5280 5000 492 508 520 536 100 2105 56 2050 4.447 2400 2345 .225 4.616 2.153 2.207
7 1221 3976 105 86 1116 3890 1203 4095 110 96 1098 4009 0 0 289 629 33 61 100 100 100 100 5006 5107 .287 3.486 3.651 3.551 3.542 1.2 80 656 3.513 .844 110 5690 4980 492 503 563 574 100 1858 40 1818 1.629 1913 1873 .614 1.706 .704 .771
8 336 791 113 88 223 703 339 870 144 104 226 782 0 0 95 263 287 140 23 97 0 90 926 1008 .317 3.152 3.46 3.183 3.209 1.506 120 820 3.251 .81 120 6080 4970 491 503 602 614 100 370 41 328 1.473 407 365 .679 1.617 .559 .693
9 258 272 109 83 149 189 216 245 121 88 107 162 0 0 228 200 50 26 80 100 56 96 338 269 .788 1.268 1.514 1.575 1.286 2.112 80 560 1.081 .765 100 6460 4970 492 502 641 651 0 127 39 88 .593 114 76 1.687 .707 -.755 -.499
10 451 765 105 84 346 681 461 827 109 86 356 743 0 0 114 218 26 20 100 100 99 100 1027 1099 .508 1.968 2.087 1.949 1.955 1.351 120 820 1.982 .922 120 6820 4970 491 503 676 688 100 357 39 318 .92 386 347 1.087 .975 -.121 -.036
11 525 1198 112 86 413 1112 542 1277 118 91 430 1191 0 0 174 397 32 29 99 100 99 100 1525 1621 .371 2.692 2.77 2.792 2.799 1.387 120 820 2.677 .911 120 7220 4970 491 503 716 728 100 560 40 520 1.258 597 557 .795 1.294 .331 .372
12 3339 4296 106 81 3233 4215 3572 4342 110 82 3466 4261 0 0 903 865 27 16 100 100 100 100 7448 7727 .767 1.304 1.229 1.363 1.294 1.329 120 820 1.277 .956 120 7600 4970 491 503 754 766 100 2007 38 1970 .609 2029 1991 1.642 .574 -.715 -.8
13 495 672 106 82 389 590 509 687 113 85 403 605 0 0 123 150 39 20 100 100 100 100 979 1008 .659 1.517 1.501 1.551 1.535 1.348 120 820 1.503 .904 120 7990 4980 492 504 793 805 100 314 38 276 .709 321 283 1.411 .701 -.497 -.512
14 3208 5708 108 81 3100 5627 3335 5666 118 89 3227 5585 0 0 737 974 72 37 100 100 100 100 8727 8812 .551 1.815 1.731 1.855 1.7 1.319 120 820 1.81 .932 120 8380 4980 492 504 832 844 100 2667 38 2629 .848 2648 2610 1.179 .809 -.238 -.306
15 408 684 110 81 298 603 398 677 116 84 288 596 0 0 126 148 37 21 97 100 96 100 901 884 .494 2.023 2.069 2.157 2.022 1.483 156 1140 1.938 .839 140 8750 4980 491 505 868 882 100 320 38 282 .946 316 278 1.058 .967 -.081 -.048
16 2934 2304 110 82 2824 2222 3040 2380 116 86 2930 2298 0 0 792 605 43 27 100 100 100 100 5046 5228 1.271 .787 .784 .783 .796 1.23 156 1140 .783 .97 140 9130 4970 490 504 906 920 100 1077 38 1038 .368 1112 1074 2.72 .366 -1.444 -1.448
17 390 615 109 81 281 534 378 617 124 87 269 536 0 0 106 123 140 48 92 100 42 100 815 805 .526 1.9 1.993 1.971 1.934 1.327 120 940 1.12 .433 130 9510 4980 491 504 944 957 100 287 38 250 .888 288 250 1.126 .931 -.171 -.103
18 2135 3584 109 81 2026 3503 2331 3779 112 83 2222 3698 0 0 745 1143 24 17 100 100 99 100 5529 5920 .578 1.729 1.664 1.839 1.728 1.43 120 820 1.711 .97 120 9900 4970 491 503 984 996 100 1675 38 1637 .808 1766 1728 1.238 .778 -.308 -.363
19 910 961 108 78 802 883 887 940 110 80 779 862 0 0 256 213 25 20 100 100 100 100 1685 1641 .908 1.101 1.107 1.143 1.123 1.271 156 1272 1.071 .945 150 10280 4980 490 505 1020 1035 100 449 36 413 .514 439 403 1.944 .517 -.959 -.952
20 9846 9203 109 80 9737 9123 10150 9806 115 83 10041 9726 0 0 1932 2323 43 21 100 100 100 100 18860 19767 1.067 .937 .969 .913 .968 1.241 120 940 .953 .971 130 10660 4970 490 503 1059 1072 100 4300 37 4263 .438 4582 4545 2.284 .453 -1.192 -1.144

Total number of rows: 24288

Table truncated, full table size 5463 Kbytes.




Supplementary file Size Download File type/resource
GSM498989.gpr.gz 2.1 Mb (ftp)(http) GPR
Processed data included within Sample table
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