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Sample GSM498990 Query DataSets for GSM498990
Status Public on Jan 21, 2010
Title AD4_REP2_ROOT
Sample type RNA
 
Channel 1
Source name AD4 no-salt root
Organism Gossypium mustelinum
Characteristics treatment: no-salt
name: 15-c
genome: ad4
polyploid level: 4x
tissue type: root
Treatment protocol BYU growth chamber
Extracted molecule total RNA
Extraction protocol Date performed = 10/31/2007; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD4 no-salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 3 plants"
Label Cy3
Label protocol Approx RNA yield = 10 ug; Type of in-vitro transcription = Epicentre; Date performed = 1/9/2008; 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 root; Date performed = 2/18/2008; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura
 
Channel 2
Source name AD4 salt root
Organism Gossypium mustelinum
Characteristics treatment: salt
name: 15-c
genome: ad4
tissue type: root
polyploid level: 4x
Treatment protocol BYU growth chamber
Extracted molecule total RNA
Extraction protocol Date performed = 10/31/2007; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD4 salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 3 plants"; Name = Rozaura; Extracted molecule = RNA
Label Cy5
Label protocol Approx RNA yield = 15 ug; Date performed = 1/9/2008; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 2/18/2008; Tube label = AD4 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 = 2/22/2008
Scanner Make = Agilent; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 2/22/2008
Description Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58088.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 4579 1650 110 56 4469 1594 4906 1743 112 57 4796 1687 0 0 1322 471 20 10 100 100 100 100 6063 6483 2.804 .357 .352 .358 .359 1.14 120 820 .353 .983 120 4010 4200 414 426 395 407 100 2277 77 2199 .492 2405 2328 2.032 .485 -1.023 -1.043
2 189 91 105 55 84 36 172 87 109 57 67 32 0 0 77 30 34 18 77 70 48 41 120 99 2.333 .429 .478 .423 .446 2.111 80 656 .386 .691 110 4390 4230 417 428 433 444 0 126 76 50 .591 120 44 1.691 .659 -.758 -.602
3 12974 5241 108 56 12866 5185 13631 5522 111 57 13523 5466 0 0 2530 978 21 10 100 100 100 100 18051 18989 2.481 .403 .404 .404 .405 1.102 120 940 .399 .987 130 4770 4210 414 427 470 483 100 7231 77 7154 .556 7619 7542 1.798 .558 -.847 -.842
4 1276 464 110 56 1166 408 1289 473 111 57 1179 417 0 0 179 81 21 10 100 100 100 100 1574 1596 2.858 .35 .354 .346 .362 1.179 120 940 .346 .961 130 5150 4210 414 427 508 521 100 640 77 563 .483 653 575 2.071 .488 -1.05 -1.035
5 397 271 104 55 293 216 386 276 109 58 282 221 0 0 98 68 53 24 100 100 98 100 509 503 1.356 .737 .784 .745 .72 1.293 80 656 .666 .875 110 5540 4210 415 426 548 559 100 374 76 298 1.017 381 305 .983 1.081 .025 .113
6 2602 1049 109 59 2493 990 473 530 111 62 364 471 0 0 2841 834 20 17 59 100 57 100 3483 835 2.518 .397 1.294 .931 .357 5.411 392 2976 .327 .961 230 5920 4240 412 435 580 603 100 1447 81 1366 .548 731 650 1.825 1.785 -.868 .836
7 1466 751 108 56 1358 695 1550 752 110 56 1442 696 0 0 442 262 20 9 100 100 100 100 2053 2138 1.954 .512 .483 .504 .51 1.256 120 820 .515 .964 120 6310 4220 416 428 625 637 100 1036 77 959 .706 1038 960 1.416 .666 -.502 -.586
8 4707 1771 108 55 4599 1716 5125 1924 110 56 5017 1869 0 0 1148 424 21 10 100 100 100 100 6315 6886 2.68 .373 .373 .373 .374 1.133 120 940 .37 .983 130 6690 4220 415 428 662 675 100 2444 76 2368 .515 2655 2579 1.942 .514 -.958 -.96
9 173 106 104 52 69 54 170 107 106 53 66 55 0 0 32 23 20 10 95 97 78 92 123 121 1.278 .783 .833 .776 .837 1.73 80 656 .616 .591 110 7070 4210 415 426 701 712 0 146 72 75 1.08 148 76 .926 1.15 .111 .201
10 2152 1008 92 50 2060 958 2154 1015 93 51 2062 965 0 0 710 280 23 12 100 100 100 100 3018 3027 2.15 .465 .468 .475 .49 1.549 120 820 .421 .789 120 7450 4210 415 427 739 751 100 1391 69 1322 .642 1400 1332 1.558 .646 -.64 -.631
11 810 588 103 55 707 533 864 628 104 56 761 573 0 0 332 258 19 12 100 100 98 100 1240 1334 1.326 .754 .753 .761 .759 1.294 120 820 .75 .965 120 7840 4210 415 427 778 790 100 811 76 735 1.04 867 791 .961 1.039 .057 .055
12 51599 13965 110 56 51489 13909 54130 14387 116 56 54020 14331 0 0 9498 2511 68 10 100 100 100 100 65398 68351 3.702 .27 .265 .27 .269 1.077 120 940 .268 .98 130 8220 4200 413 426 815 828 100 19269 77 19192 .373 19851 19774 2.683 .366 -1.424 -1.45
13 350 217 107 56 243 161 351 223 109 56 244 167 0 0 70 43 21 10 100 100 100 100 404 411 1.509 .663 .684 .661 .669 1.28 120 940 .633 .906 130 8600 4230 416 429 853 866 100 299 77 222 .914 308 230 1.094 .944 -.129 -.083
14 5955 2038 109 58 5846 1980 6025 2065 110 59 5916 2007 0 0 1079 386 19 10 100 100 100 100 7826 7923 2.953 .339 .339 .338 .345 1.166 120 820 .338 .981 120 9000 4220 416 428 894 906 100 2812 80 2732 .467 2849 2769 2.14 .468 -1.097 -1.095
15 1253 447 107 58 1146 389 1244 449 109 59 1137 391 0 0 193 77 19 10 100 100 100 100 1535 1528 2.946 .339 .344 .337 .336 1.186 156 1272 .334 .959 150 9360 4220 414 429 928 943 100 617 80 537 .468 620 539 2.135 .474 -1.094 -1.076
16 1670 513 109 56 1561 457 1569 493 110 57 1460 437 0 0 859 228 19 10 100 100 100 99 2018 1897 3.416 .293 .299 .294 .304 1.243 156 1272 .277 .94 150 9750 4220 414 429 967 982 100 708 77 631 .404 680 603 2.476 .413 -1.308 -1.276
17 462 261 107 56 355 205 451 263 108 57 344 207 0 0 74 41 19 10 100 100 100 100 560 551 1.732 .577 .602 .577 .587 1.259 156 1272 .547 .908 150 10130 4230 415 430 1005 1020 100 360 77 283 .797 363 286 1.255 .83 -.328 -.268
18 6381 2118 109 56 6272 2062 6698 2234 111 57 6589 2178 0 0 1401 508 24 11 100 100 100 100 8334 8767 3.042 .329 .331 .325 .33 1.108 120 820 .33 .988 120 10500 4210 415 427 1044 1056 100 2922 77 2845 .454 3082 3005 2.204 .456 -1.14 -1.133
19 2048 724 110 57 1938 667 1999 724 112 58 1889 667 0 0 541 194 25 13 100 100 100 100 2605 2556 2.906 .344 .353 .343 .34 1.121 156 1272 .342 .971 150 10900 4220 414 429 1082 1097 100 999 79 920 .475 999 920 2.106 .487 -1.074 -1.037
20 23997 12227 111 57 23886 12170 23687 12528 115 61 23576 12471 0 0 3926 2384 58 35 100 100 100 100 36056 36047 1.963 .51 .529 .504 .519 1.168 120 940 .512 .973 130 11270 4230 416 429 1120 1133 100 16871 79 16792 .703 17286 17207 1.422 .73 -.508 -.454

Total number of rows: 24288

Table truncated, full table size 5430 Kbytes.




Supplementary file Size Download File type/resource
GSM498990.gpr.gz 2.1 Mb (ftp)(http) GPR
Processed data included within Sample table
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