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Sample GSM498991 Query DataSets for GSM498991
Status Public on Jan 21, 2010
Title AD4_REP3_LEAF
Sample type RNA
 
Channel 1
Source name AD4 salt leaf
Organism Gossypium mustelinum
Characteristics treatment: 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 = Jun-07; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD4 salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"
Label Cy3
Label protocol Approx RNA yield = 13 ug; Type of in-vitro transcription = Epicentre; Date performed = Jul-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 salt leaf; Date performed = 7/23/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura
 
Channel 2
Source name AD4 no-salt leaf
Organism Gossypium mustelinum
Characteristics treatment: no-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 = Jun-07; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD4 no-salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"; Name = Rozaura; Extracted molecule = RNA
Label Cy5
Label protocol Approx RNA yield = 12 ug; Date performed = Jul-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 = 7/23/2007; Tube label = AD4 no-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 = 7/26/2007
Scanner Make = Agilent; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 7/26/2007
Description Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58089.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 1724 3066 94 67 1630 2999 1663 3282 100 70 1569 3215 0 0 1489 1423 42 25 100 100 100 100 4629 4784 .544 1.84 2.049 1.964 2.021 1.307 120 820 1.5 .806 120 3810 4100 404 416 375 387 100 1443 32 1411 .866 1545 1513 1.155 .964 -.208 -.052
2 1431 2415 92 68 1339 2347 1136 1712 103 80 1044 1644 0 0 859 1778 54 57 100 100 100 100 3686 2688 .571 1.753 1.575 1.643 1.613 1.36 120 820 1.898 .948 120 4190 4080 402 414 413 425 100 1137 32 1105 .825 806 774 1.212 .741 -.278 -.432
3 3928 4833 94 66 3834 4767 3990 5048 112 73 3896 4982 0 0 1226 1490 210 66 99 100 98 100 8601 8878 .804 1.243 1.279 1.268 1.253 1.258 120 940 1.244 .979 130 4560 4080 401 414 449 462 100 2275 31 2244 .585 2376 2345 1.709 .602 -.773 -.733
4 468 709 92 67 376 642 456 716 94 68 364 649 0 0 160 186 23 13 99 100 98 100 1018 1013 .586 1.707 1.783 1.77 1.788 1.349 120 940 1.655 .883 130 4950 4090 402 415 488 501 100 334 32 302 .804 337 305 1.244 .839 -.315 -.253
5 1414 1766 90 66 1324 1700 1403 1758 94 68 1313 1692 0 0 120 185 30 16 100 100 100 100 3024 3005 .779 1.284 1.289 1.281 1.27 1.111 80 656 1.304 .976 110 5330 4090 403 414 527 538 100 831 31 800 .604 827 796 1.655 .606 -.727 -.721
6 910 1876 89 66 821 1810 114 341 92 70 25 275 0 0 1128 2217 26 23 49 99 43 99 2631 300 .454 2.205 11 5.342 2.924 3.441 460 3236 2.046 .98 240 5710 4100 398 422 559 583 100 883 31 852 1.038 160 129 .964 5.177 .053 2.372
7 871 1756 90 65 781 1691 952 1946 99 74 862 1881 0 0 341 619 107 81 95 100 90 99 2472 2743 .462 2.165 2.182 2.354 2.193 1.406 120 820 2.118 .971 120 6100 4100 404 416 604 616 100 826 31 796 1.019 916 885 .981 1.027 .027 .038
8 288 424 89 63 199 361 289 450 90 64 200 387 0 0 75 110 16 12 100 100 99 100 560 587 .551 1.814 1.935 1.836 1.866 1.433 120 820 1.817 .83 120 6470 4080 402 414 641 653 100 200 30 170 .854 212 182 1.171 .911 -.228 -.135
9 158 147 88 64 70 83 104 115 89 64 16 51 0 0 160 119 16 12 49 82 35 73 153 67 .843 1.186 3.188 1.799 1.781 3.103 156 1140 .779 .718 140 6870 4070 400 414 680 694 0 69 30 39 .558 54 24 1.792 1.5 -.842 .585
10 801 1115 86 62 715 1053 893 1289 91 64 807 1227 0 0 250 433 59 25 99 100 97 99 1768 2034 .679 1.473 1.52 1.401 1.511 1.437 120 820 1.476 .888 120 7240 4090 403 415 718 730 100 525 29 496 .693 607 577 1.443 .716 -.529 -.483
11 642 1104 86 62 556 1042 629 1158 88 63 543 1096 0 0 109 195 19 12 100 100 100 100 1598 1639 .534 1.874 2.018 1.869 1.92 1.229 80 656 1.894 .927 110 7640 4090 403 414 758 769 100 520 29 490 .882 545 516 1.134 .95 -.181 -.074
12 3570 5397 88 61 3482 5336 3723 5814 105 68 3635 5753 0 0 1464 1666 206 65 98 100 97 100 8818 9388 .653 1.532 1.583 1.664 1.573 1.638 120 820 1.475 .932 120 8020 4090 403 415 796 808 100 2540 29 2511 .721 2736 2708 1.387 .745 -.471 -.425
13 314 484 89 63 225 421 242 446 90 64 153 383 0 0 441 322 18 11 99 100 96 100 646 536 .534 1.871 2.503 2.577 2.66 1.51 120 940 1.018 .711 130 8390 4080 401 414 832 845 100 228 30 198 .881 210 180 1.136 1.178 -.183 .237
14 4946 7797 89 64 4857 7733 5326 8324 98 83 5237 8260 0 0 1321 2023 106 232 100 100 100 100 12590 13497 .628 1.592 1.577 1.599 1.571 1.118 120 940 1.593 .984 130 8790 4090 402 415 872 885 100 3670 30 3639 .749 3918 3888 1.335 .742 -.416 -.43
15 371 693 88 62 283 631 369 720 89 63 281 658 0 0 93 167 16 11 100 100 99 100 914 939 .448 2.23 2.342 2.27 2.298 1.327 156 1140 2.228 .908 140 9160 4080 401 415 909 923 100 326 29 297 1.049 339 310 .953 1.102 .07 .14
16 4931 8949 89 63 4842 8886 5198 9256 95 67 5109 9193 0 0 1377 2312 74 42 100 100 100 100 13728 14302 .545 1.835 1.799 1.86 1.82 1.197 156 1140 1.835 .974 140 9540 4070 400 414 947 961 100 4212 30 4182 .864 4356 4327 1.158 .847 -.211 -.24
17 480 666 89 64 391 602 244 341 93 67 155 277 0 0 646 912 32 22 87 91 82 89 993 432 .65 1.54 1.787 1.679 1.618 1.529 208 1512 1.446 .967 160 9900 4100 402 418 982 998 100 313 30 283 .725 160 130 1.38 .841 -.465 -.25
18 3100 5872 90 63 3010 5809 3501 6370 92 63 3411 6307 0 0 1079 1685 16 11 100 100 100 100 8819 9718 .518 1.93 1.849 2.03 1.891 1.309 120 820 1.892 .973 120 10300 4060 400 412 1024 1036 100 2764 30 2734 .908 2998 2968 1.101 .87 -.139 -.201
19 623 1003 90 63 533 940 600 1002 112 79 510 939 0 0 145 221 324 223 96 100 17 97 1473 1449 .567 1.764 1.841 1.767 1.822 1.236 156 1140 1.034 .731 140 10660 4080 401 415 1059 1073 100 472 30 442 .83 472 442 1.205 .867 -.269 -.207
20 9891 11829 92 64 9799 11765 10703 12471 93 64 10611 12407 0 0 2684 2440 20 12 100 100 100 100 21564 23018 .833 1.201 1.169 1.242 1.16 1.293 120 820 1.178 .971 120 11050 4070 401 413 1099 1111 100 5567 30 5537 .565 5869 5839 1.77 .55 -.823 -.862

Total number of rows: 24288

Table truncated, full table size 5431 Kbytes.




Supplementary file Size Download File type/resource
GSM498991.gpr.gz 2.1 Mb (ftp)(http) GPR
Processed data included within Sample table
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