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Sample GSM498976 Query DataSets for GSM498976
Status Public on Jan 21, 2010
Title AD1_REP1_LEAF
Sample type RNA
 
Channel 1
Source name AD1 no-salt leaf
Organism Gossypium hirsutum
Characteristics treatment: no-salt
name: tm1
genome: ad1
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 = AD1 no-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 = 10 ug; Type of in-vitro transcription = Epicentre; Date performed = Jun-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 = AD1 no-salt leaf; Date performed = 6/8/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura
 
Channel 2
Source name AD1 salt leaf
Organism Gossypium hirsutum
Characteristics treatment: salt
name: tm1
genome: ad1
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 = AD1 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 = 22 ug; Date performed = Jun-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 = 6/8/2007; Tube label = AD1 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 = 6/11/2007
Scanner Make = Agilent; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 6/11/2007
Description Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58064.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 1839 2700 135 84 1704 2616 2053 3059 137 86 1918 2975 0 0 586 841 28 16 100 100 100 100 4320 4893 .651 1.535 1.551 1.533 1.529 1.213 120 820 1.524 .979 120 3860 3620 356 368 380 392 100 1869 58 1810 1.062 2117 2059 .941 1.073 .087 .102
2 4983 5080 137 88 4846 4992 3404 3413 146 96 3267 3325 0 0 3790 3889 51 45 100 100 100 100 9838 6592 .971 1.03 1.018 1.01 1.019 1.185 120 940 1.029 .989 130 4270 3620 355 368 420 433 100 3516 61 3455 .713 2362 2301 1.403 .704 -.488 -.506
3 7734 9798 138 86 7596 9712 7758 10061 141 87 7620 9975 0 0 2468 3017 27 16 100 100 100 100 17308 17595 .782 1.279 1.309 1.273 1.295 1.171 120 940 1.276 .98 130 4650 3640 357 370 458 471 100 6781 60 6721 .885 6963 6903 1.13 .906 -.177 -.143
4 669 849 138 86 531 763 671 870 143 87 533 784 0 0 122 161 31 17 100 100 99 100 1294 1317 .696 1.437 1.471 1.445 1.482 1.218 120 820 1.402 .879 120 5020 3630 357 369 496 508 100 588 60 528 .994 602 543 1.006 1.018 -.008 .026
5 4973 4200 141 86 4832 4114 5421 4549 142 87 5280 4463 0 0 1236 985 27 15 100 100 100 100 8946 9743 1.175 .851 .845 .861 .854 1.164 120 820 .845 .985 120 5390 3630 357 369 533 545 100 2907 60 2847 .589 3148 3089 1.697 .585 -.763 -.774
6 2452 2595 137 89 2315 2506 2225 2149 144 99 2088 2060 0 0 2125 2157 146 116 65 99 63 74 4821 4148 .924 1.083 .987 1.579 1.089 2.698 316 2560 1.037 .982 210 5780 3640 353 374 567 588 100 1796 62 1734 .749 1487 1426 1.335 .683 -.417 -.551
7 830 1288 136 86 694 1202 897 1429 138 87 761 1343 0 0 279 472 27 16 98 100 98 100 1896 2104 .577 1.732 1.765 1.796 1.769 1.328 120 940 1.734 .972 130 6160 3630 356 369 609 622 100 891 60 832 1.199 989 929 .834 1.221 .261 .288
8 407 557 135 84 272 473 403 568 137 84 268 484 0 0 59 78 25 15 100 100 100 100 745 752 .575 1.739 1.806 1.757 1.774 1.242 80 656 1.711 .901 110 6550 3630 357 368 649 660 100 385 58 327 1.203 393 335 .831 1.25 .267 .322
9 197 144 148 88 49 56 188 140 157 88 40 52 0 0 46 31 47 16 45 88 17 76 105 92 .875 1.143 1.3 1.195 1.224 4.239 80 656 .158 .067 110 6910 3610 355 366 685 696 0 100 61 39 .791 97 36 1.264 .9 -.338 -.153
10 1418 1675 137 84 1281 1591 1400 1672 139 86 1263 1588 0 0 111 145 26 20 100 100 100 100 2872 2851 .805 1.242 1.257 1.241 1.245 1.108 80 656 1.244 .967 110 7300 3620 356 367 724 735 100 1159 58 1101 .86 1157 1099 1.163 .87 -.218 -.201
11 568 918 149 82 419 836 571 982 150 84 422 900 0 0 89 216 29 17 100 100 100 100 1255 1322 .501 1.995 2.133 1.955 2.025 1.235 80 656 2.011 .893 110 7690 3650 359 370 763 774 100 635 57 579 1.381 680 623 .724 1.476 .465 .562
12 5941 6385 155 88 5786 6297 6374 7171 158 90 6219 7083 0 0 1542 2024 32 19 100 100 100 100 12083 13302 .919 1.088 1.139 1.04 1.109 1.296 120 820 1.109 .978 120 8080 3640 358 370 802 814 100 4419 61 4358 .753 4963 4902 1.328 .788 -.409 -.343
13 779 784 158 88 621 696 727 755 161 90 569 667 0 0 263 251 33 16 100 100 100 100 1317 1236 .892 1.121 1.172 1.119 1.149 1.243 120 940 1.096 .925 130 8460 3630 356 369 839 852 100 543 61 482 .776 522 462 1.289 .811 -.367 -.302
14 2513 3854 163 88 2350 3766 2633 4097 164 89 2470 4009 0 0 521 919 29 15 100 100 100 100 6116 6479 .624 1.603 1.623 1.59 1.627 1.159 120 820 1.616 .982 120 8840 3620 356 368 878 890 100 2667 61 2606 1.109 2835 2774 .902 1.123 .149 .168
15 963 990 159 89 804 901 995 1036 162 90 836 947 0 0 239 280 30 17 100 100 99 100 1705 1783 .892 1.121 1.133 1.117 1.133 1.236 156 1140 1.126 .957 140 9210 3640 357 371 914 928 100 685 62 624 .776 717 655 1.289 .784 -.367 -.351
16 6335 5357 164 90 6171 5267 6526 5714 165 91 6362 5624 0 0 1765 1703 26 15 100 100 100 100 11438 11986 1.172 .854 .884 .832 .869 1.223 156 1140 .863 .979 140 9600 3650 358 372 953 967 100 3707 62 3645 .591 3954 3892 1.693 .612 -.76 -.709
17 423 378 165 91 258 287 371 363 170 94 206 272 0 0 258 161 47 47 98 99 96 97 545 478 .899 1.112 1.32 1.215 1.286 1.536 156 1140 .852 .81 140 9980 3640 357 371 991 1005 100 262 63 199 .77 251 188 1.299 .914 -.377 -.13
18 3512 5085 168 92 3344 4993 3505 5130 193 116 3337 5038 0 0 412 687 319 236 100 100 100 100 8337 8375 .67 1.493 1.51 1.488 1.504 1.11 80 656 1.519 .973 110 10370 3640 358 369 1031 1042 100 3519 64 3455 1.033 3550 3487 .968 1.045 .047 .063
19 2226 1751 168 90 2058 1661 2320 1834 179 96 2152 1744 0 0 859 681 167 66 96 99 94 98 3719 3896 1.239 .807 .81 .822 .814 1.375 208 1512 .786 .962 160 10740 3630 355 371 1066 1082 100 1212 62 1149 .559 1269 1207 1.79 .561 -.84 -.834
20 24099 18892 175 90 23924 18802 26170 20137 178 91 25995 20047 0 0 7375 4994 37 19 100 100 100 100 42726 46042 1.272 .786 .771 .812 .775 1.226 120 820 .772 .98 120 11130 3630 357 369 1107 1119 100 13074 62 13012 .544 13936 13873 1.839 .534 -.879 -.906

Total number of rows: 24288

Table truncated, full table size 5569 Kbytes.




Supplementary file Size Download File type/resource
GSM498976.gpr.gz 2.2 Mb (ftp)(http) GPR
Processed data included within Sample table
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