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Sample GSM498985 Query DataSets for GSM498985
Status Public on Jan 21, 2010
Title AD3_REP4_ROOT
Sample type RNA
 
Channel 1
Source name AD3 no-salt root
Organism Gossypium tomentosum
Characteristics treatment: no-salt
name: wt936
genome: ad3
polyploid level: 4x
tissue type: root
Treatment protocol BYU growth chamber
Extracted molecule total RNA
Extraction protocol Date performed = 10/15/2007; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD3 no-salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 2 plants"
Label Cy3
Label protocol Approx RNA yield = 9 ug; Type of in-vitro transcription = Epicentre; Date performed = 11/28/2007; 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 no-salt root; Date performed = 11/29/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura
 
Channel 2
Source name AD3 salt root
Organism Gossypium tomentosum
Characteristics treatment: salt
name: wt936
genome: ad3
tissue type: root
polyploid level: 4x
Treatment protocol BYU growth chamber
Extracted molecule total RNA
Extraction protocol Date performed = 10/15/2007; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD3 salt root; 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 = 18 ug; Date performed = 11/28/2007; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 11/29/2007; Tube label = AD3 salt root; 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 = 12/4/2007
Scanner Make = Agilent; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 12/4/2007
Description Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58084.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 23190 4249 111 65 23079 4184 24215 4426 119 67 24104 4361 0 0 6410 1092 60 15 100 100 100 100 27263 28465 5.516 .181 .181 .181 .183 1.169 120 940 .179 .983 130 4360 4580 451 464 429 442 100 4703 72 4631 .201 4899 4827 4.983 .2 -2.317 -2.32
2 2184 388 107 64 2077 324 1631 317 111 65 1524 253 0 0 1766 238 27 14 100 99 100 98 2401 1777 6.41 .156 .166 .168 .162 1.365 120 820 .142 .951 120 4740 4590 453 465 468 480 100 429 71 359 .173 351 280 5.791 .184 -2.534 -2.444
3 25692 5836 113 64 25579 5772 28358 6638 115 66 28245 6574 0 0 10561 2253 27 14 100 100 100 100 31351 34819 4.432 .226 .233 .231 .23 1.209 156 1140 .222 .984 140 5120 4590 452 466 505 519 100 6460 71 6389 .25 7348 7277 4.004 .258 -2.001 -1.957
4 7223 1453 106 65 7117 1388 6955 1400 113 69 6849 1335 0 0 2387 358 49 23 100 100 100 100 8505 8184 5.128 .195 .195 .2 .195 1.212 120 940 .184 .955 130 5510 4600 453 466 544 557 100 1608 72 1536 .216 1550 1478 4.632 .216 -2.212 -2.213
5 7301 1486 109 65 7192 1421 7862 1536 133 71 7753 1471 0 0 3451 616 369 73 95 98 94 97 8613 9224 5.061 .198 .19 .213 .197 1.452 156 1272 .191 .974 150 5850 4600 452 467 577 592 100 1645 72 1573 .219 1700 1628 4.572 .21 -2.193 -2.251
6 3669 1099 107 68 3562 1031 487 445 119 74 380 377 0 0 4378 945 241 51 51 100 48 100 4593 757 3.455 .289 .992 .936 .286 6.761 392 3005 .234 .939 230 6240 4610 449 472 612 635 100 1216 75 1141 .32 493 417 3.121 1.098 -1.642 .135
7 7911 1794 109 65 7802 1729 8085 1916 113 68 7976 1851 0 0 3325 788 29 20 100 100 100 100 9531 9827 4.512 .222 .232 .221 .224 1.351 120 820 .222 .969 120 6670 4610 455 467 661 673 100 1986 72 1914 .245 2121 2049 4.077 .257 -2.027 -1.961
8 11099 2953 110 66 10989 2887 11630 3171 112 67 11520 3105 0 0 3010 882 26 12 100 100 100 100 13876 14625 3.806 .263 .27 .258 .267 1.218 120 940 .263 .98 130 7050 4590 452 465 698 711 100 3269 73 3196 .291 3510 3437 3.439 .298 -1.782 -1.745
9 2008 551 105 66 1903 485 1690 481 111 67 1585 415 0 0 1053 244 42 15 100 100 100 100 2388 2000 3.924 .255 .262 .259 .264 1.251 80 656 .245 .957 110 7420 4590 453 464 736 747 100 610 73 537 .282 532 459 3.545 .29 -1.826 -1.787
10 5482 1342 110 64 5372 1278 6017 1485 114 66 5907 1421 0 0 1936 462 41 15 100 99 99 98 6650 7328 4.203 .238 .241 .232 .244 1.303 120 820 .235 .981 120 7780 4590 453 465 772 784 100 1485 71 1415 .263 1644 1573 3.798 .266 -1.925 -1.909
11 3421 1024 107 66 3314 958 3451 1094 113 68 3344 1028 0 0 1521 446 38 15 100 100 100 100 4272 4372 3.459 .289 .307 .278 .282 1.396 120 820 .284 .96 120 8190 4590 453 465 813 825 100 1133 73 1060 .32 1211 1138 3.125 .34 -1.644 -1.555
12 17131 4379 112 66 17019 4313 18164 4654 114 67 18052 4588 0 0 3974 1135 23 15 100 100 100 100 21332 22640 3.946 .253 .254 .249 .258 1.154 120 940 .253 .982 130 8570 4580 451 464 850 863 100 4847 73 4774 .281 5151 5078 3.565 .281 -1.834 -1.83
13 1715 546 107 65 1608 481 1653 553 109 66 1546 488 0 0 460 110 20 13 100 100 100 100 2089 2034 3.343 .299 .316 .304 .319 1.226 120 940 .286 .944 130 8960 4600 453 466 889 902 100 604 72 532 .331 612 540 3.02 .349 -1.595 -1.517
14 4933 1075 108 65 4825 1010 5096 1113 111 66 4988 1048 0 0 1091 250 24 12 100 100 100 100 5835 6036 4.777 .209 .21 .206 .209 1.15 120 940 .209 .959 130 9340 4600 453 466 927 940 100 1190 72 1118 .232 1232 1160 4.316 .233 -2.11 -2.104
15 1109 440 110 67 999 373 1028 429 113 68 918 362 0 0 327 90 30 15 100 100 100 100 1372 1280 2.678 .373 .394 .381 .388 1.242 156 1272 .348 .924 150 9730 4600 452 467 965 980 100 487 74 413 .413 475 401 2.42 .436 -1.275 -1.196
16 1333 590 111 68 1222 522 1264 600 119 84 1153 532 0 0 418 146 43 66 100 99 100 98 1744 1685 2.341 .427 .461 .429 .437 1.281 156 1272 .41 .941 150 10110 4590 451 466 1003 1018 100 653 75 578 .473 664 589 2.115 .511 -1.081 -.969
17 648 389 111 68 537 321 630 385 112 69 519 317 0 0 171 71 22 12 100 100 100 100 858 836 1.673 .598 .611 .616 .622 1.336 156 1140 .563 .908 140 10480 4600 453 467 1041 1055 100 431 75 355 .662 426 351 1.511 .676 -.596 -.565
18 8639 1409 115 65 8524 1344 8745 1404 119 66 8630 1339 0 0 978 180 33 12 100 100 100 100 9868 9969 6.342 .158 .155 .157 .158 1.101 80 656 .154 .963 110 10860 4580 452 463 1080 1091 100 1560 72 1488 .175 1554 1482 5.73 .172 -2.518 -2.542
19 1388 492 113 72 1275 420 1363 466 116 74 1250 394 0 0 250 125 24 16 100 100 100 100 1695 1644 3.036 .329 .315 .322 .323 1.271 156 1272 .331 .894 150 11230 4600 452 467 1115 1130 100 545 80 465 .365 516 436 2.743 .349 -1.456 -1.519
20 15458 4950 113 67 15345 4883 17424 5722 117 70 17311 5655 0 0 6256 1978 28 19 100 100 100 100 20228 22966 3.143 .318 .327 .321 .323 1.208 156 1140 .317 .99 140 11650 4590 452 466 1158 1172 100 5479 74 5405 .352 6334 6259 2.839 .362 -1.505 -1.468

Total number of rows: 24288

Table truncated, full table size 5462 Kbytes.




Supplementary file Size Download File type/resource
GSM498985.gpr.gz 2.1 Mb (ftp)(http) GPR
Processed data included within Sample table
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