NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM498983 Query DataSets for GSM498983
Status Public on Jan 21, 2010
Title AD3_REP4_LEAF
Sample type RNA
 
Channel 1
Source name AD3 salt leaf
Organism Gossypium tomentosum
Characteristics treatment: salt
name: wt936
genome: ad3
polyploid level: 4x
tissue type: leaf
Treatment protocol BYU growth chamber
Extracted molecule total RNA
Extraction protocol Date performed = Jul-07; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD3 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 = 15 ug; Type of in-vitro transcription = Epicentre; Date performed = Aug-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 = AD3 salt leaf; Date performed = 8/17/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura
 
Channel 2
Source name AD3 no-salt leaf
Organism Gossypium tomentosum
Characteristics treatment: no-salt
name: wt936
genome: ad3
tissue type: leaf
polyploid level: 4x
Treatment protocol BYU growth chamber
Extracted molecule total RNA
Extraction protocol Date performed = Jul-07; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD3 no-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 = 10 ug; Date performed = Aug-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 = 8/17/2007; Tube label = AD3 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 = 8/28/2007
Scanner Make = Agilent; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 8/28/2007
Description Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58083.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
1 991 3379 100 100 891 3279 949 3455 103 105 849 3355 0 0 278 569 26 41 100 100 100 100 4170 4204 .272 3.68 3.952 3.809 4.001 1.295 120 940 3.68 .908 130 3930 4820 475 488 386 399 100 711 21 690 .774 727 706 1.292 .831 -.369 -.267
2 1301 5829 98 98 1203 5731 940 4071 105 131 842 3973 0 0 953 4622 43 187 100 100 100 100 6934 4815 .21 4.764 4.719 4.7 4.776 1.213 120 940 4.878 .971 130 4320 4820 475 488 425 438 100 1226 21 1206 1.002 856 836 .998 .993 .003 -.011
3 3053 8918 95 94 2958 8824 3343 9794 100 110 3248 9700 0 0 1070 3161 31 117 100 100 100 100 11782 12948 .335 2.983 2.986 2.987 2.973 1.32 156 1140 3 .98 140 4700 4830 476 490 463 477 100 1876 20 1856 .628 2060 2041 1.594 .628 -.672 -.671
4 440 1677 96 93 344 1584 442 1623 97 94 346 1530 0 0 82 291 16 17 100 100 100 100 1928 1876 .217 4.605 4.422 4.675 4.647 1.2 120 940 4.593 .944 130 5090 4840 477 490 502 515 100 353 20 333 .969 341 322 1.032 .93 -.046 -.104
5 551 1640 95 94 456 1546 588 1793 97 94 493 1699 0 0 138 438 16 15 99 100 99 100 2002 2192 .295 3.39 3.446 3.457 3.419 1.264 120 820 3.389 .966 120 5460 4830 477 489 540 552 100 345 20 325 .713 377 357 1.402 .725 -.488 -.464
6 892 1633 97 99 795 1534 120 347 99 103 23 248 0 0 1073 1754 20 37 51 100 46 99 2329 271 .518 1.93 10.783 4.254 2.271 3.33 460 3430 1.74 .958 250 5850 4850 472 497 572 597 100 344 21 323 .406 73 52 2.464 2.268 -1.301 1.182
7 1194 3996 95 92 1099 3904 1221 4183 96 93 1126 4091 0 0 419 1273 16 16 100 100 100 100 5003 5217 .282 3.552 3.633 3.639 3.612 1.234 120 820 3.498 .971 120 6240 4820 476 488 618 630 100 841 19 821 .747 880 861 1.338 .764 -.42 -.388
8 301 1144 96 93 205 1051 315 1223 96 94 219 1130 0 0 69 294 16 14 99 100 98 100 1256 1349 .195 5.127 5.16 5.225 5.172 1.316 120 940 5.137 .924 130 6620 4820 475 488 655 668 100 241 20 221 1.079 257 238 .927 1.085 .109 .118
9 87 126 97 96 -10 30 86 129 98 96 -11 33 0 0 17 33 17 18 8 62 0 43 20 22 null null null 1.731 2.213 5.613 120 940 8.553 .014 130 7010 4820 475 488 694 707 -50 27 20 6 null 27 7 null null null null
10 226 866 98 97 128 769 190 938 100 99 92 841 0 0 104 225 17 19 97 100 93 100 897 933 .166 6.008 9.141 7.274 8.176 1.966 120 820 5.739 .579 120 7370 4810 475 487 731 743 100 182 20 162 1.264 197 177 .791 1.923 .338 .943
11 298 1815 100 99 198 1716 310 2007 101 99 210 1908 0 0 80 578 17 16 98 100 96 100 1914 2118 .115 8.667 9.086 9.245 8.775 1.696 120 820 8.594 .911 120 7760 4810 475 487 770 782 100 382 21 361 1.823 422 401 .548 1.911 .866 .935
12 1309 7872 102 102 1207 7770 1412 9322 121 138 1310 9220 0 0 580 3569 147 169 96 98 90 98 8977 10530 .155 6.437 7.038 6.085 7.253 1.766 156 1140 7.012 .815 140 8140 4820 475 489 807 821 100 1656 21 1635 1.354 1961 1940 .738 1.481 .437 .566
13 257 736 102 105 155 631 255 737 127 140 153 632 0 0 60 157 224 249 13 100 0 78 786 785 .246 4.071 4.131 4.325 4.116 1.388 120 940 3.737 .806 130 8540 4830 476 489 847 860 100 155 22 133 .856 155 133 1.168 .869 -.224 -.203
14 1659 9643 100 105 1559 9538 1628 9772 112 113 1528 9667 0 0 294 1394 169 153 100 100 100 100 11097 11195 .163 6.118 6.327 6.168 6.194 1.149 120 940 6.201 .964 130 8910 4820 475 488 884 897 100 2029 22 2006 1.287 2056 2034 .777 1.331 .364 .412
15 435 1494 97 98 338 1396 430 1472 99 100 333 1374 0 0 105 381 16 16 100 100 100 100 1734 1707 .242 4.13 4.126 4.155 4.275 1.318 156 1272 4.196 .926 150 9300 4830 475 490 922 937 100 314 21 294 .869 310 289 1.151 .868 -.203 -.204
16 190 542 96 96 94 446 190 549 97 97 94 453 0 0 41 122 16 16 96 100 92 100 540 547 .211 4.745 4.819 5.1 4.587 1.55 156 1140 4.729 .791 140 9680 4840 477 491 961 975 100 114 20 94 .998 115 95 1.002 1.014 -.003 .02
17 128 301 95 93 33 208 127 297 96 94 32 204 0 0 31 80 15 15 66 100 50 100 241 236 .159 6.303 6.375 7.209 5.655 2.465 156 1140 5.728 .437 140 10080 4830 476 490 1001 1015 100 63 20 44 1.326 62 43 .754 1.341 .407 .423
18 2071 13771 96 95 1975 13676 2245 14800 97 96 2149 14705 0 0 611 3803 16 15 100 100 100 100 15651 16854 .144 6.925 6.843 7.096 6.919 1.233 120 820 6.906 .979 120 10440 4810 475 487 1038 1050 100 2897 20 2877 1.457 3113 3093 .686 1.439 .543 .526
19 844 2041 96 95 748 1946 783 1937 97 97 687 1842 0 0 215 482 18 23 100 100 100 100 2694 2529 .384 2.602 2.681 2.621 2.664 1.157 156 1272 2.555 .948 150 10830 4820 474 489 1075 1090 100 429 20 409 .547 407 387 1.827 .564 -.87 -.826
20 8923 27162 97 99 8826 27063 9223 28123 98 100 9126 28024 0 0 1624 4996 17 19 100 100 100 100 35889 37150 .326 3.066 3.071 3.068 3.061 1.102 120 820 3.089 .984 120 11190 4810 475 487 1113 1125 100 5714 21 5693 .645 5916 5895 1.55 .646 -.633 -.63

Total number of rows: 24288

Table truncated, full table size 5422 Kbytes.




Supplementary file Size Download File type/resource
GSM498983.gpr.gz 2.1 Mb (ftp)(http) GPR
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap