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Sample GSM498984 Query DataSets for GSM498984
Status Public on Jan 21, 2010
Title AD1_REP3_ROOT
Sample type RNA
 
Channel 1
Source name AD1 salt root
Organism Gossypium hirsutum
Characteristics treatment: salt
name: tm1
genome: ad1
polyploid level: 4x
tissue type: root
Treatment protocol BYU growth chamber
Extracted molecule total RNA
Extraction protocol Date performed = 11/1/2007; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD1 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 = 3/30/2008; 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 = AD1 salt root; Date performed = 3/31/2008; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura
 
Channel 2
Source name AD1 no-salt root
Organism Gossypium hirsutum
Characteristics treatment: no-salt
name: tm1
genome: ad1
tissue type: root
polyploid level: 4x
Treatment protocol BYU growth chamber
Extracted molecule total RNA
Extraction protocol Date performed = 11/1/2007; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD1 no-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 = 21 ug; Date performed = 3/30/2008; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 3/31/2008; Tube label = AD1 no-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 = 4/2/2008
Scanner Make = Agilent; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 4/2/2008
Description Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58068.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 1207 390 74 53 1133 337 1301 411 80 57 1227 358 0 0 381 150 90 48 100 100 100 95 1470 1585 3.362 .297 .292 .28 .284 1.234 120 940 .305 .961 130 3760 5010 494 507 369 382 100 454 62 392 .346 478 417 2.89 .339 -1.531 -1.559
2 130 88 73 51 57 37 117 81 73 53 44 30 0 0 60 31 13 10 80 86 69 66 94 74 1.541 .649 .682 .706 .638 2.371 120 820 .502 .643 120 4150 5020 496 508 409 421 0 102 59 43 .755 94 35 1.324 .793 -.405 -.334
3 6710 1533 74 54 6636 1479 6959 1546 76 55 6885 1492 0 0 1505 423 17 10 100 100 100 100 8115 8377 4.487 .223 .217 .22 .221 1.142 120 940 .222 .965 130 4530 5020 495 508 446 459 100 1784 63 1721 .259 1799 1736 3.857 .252 -1.947 -1.988
4 710 142 72 53 638 89 718 141 74 54 646 88 0 0 102 26 13 9 100 100 100 100 727 734 7.169 .139 .136 .135 .137 1.377 120 940 .137 .849 130 4900 5030 496 509 483 496 100 165 62 104 .162 164 102 6.162 .158 -2.623 -2.658
5 175 145 73 53 102 92 175 143 73 53 102 90 0 0 42 40 13 9 99 99 97 97 194 192 1.109 .902 .882 .888 .953 1.671 120 820 .876 .762 120 5300 5030 497 509 524 536 100 169 62 107 1.049 166 105 .953 1.027 .07 .038
6 266 277 73 54 193 223 92 273 74 56 19 219 0 0 250 68 15 17 53 100 45 100 416 238 .865 1.155 11.526 2.037 .626 7.434 460 3252 .434 .207 240 5690 5040 492 516 557 581 100 322 63 259 1.344 318 255 .744 13.41 .427 3.745
7 820 334 72 52 748 282 851 327 74 55 779 275 0 0 217 107 20 26 100 100 100 100 1030 1054 2.652 .377 .353 .364 .365 1.242 120 820 .381 .916 120 6080 5030 497 509 602 614 100 389 60 328 .439 380 320 2.28 .411 -1.189 -1.284
8 2792 1370 73 54 2719 1316 3004 1437 74 54 2931 1383 0 0 635 332 13 9 100 100 100 100 4035 4314 2.066 .484 .472 .48 .483 1.136 120 940 .486 .98 130 6450 5010 494 507 638 651 100 1594 63 1531 .563 1672 1609 1.776 .549 -.829 -.865
9 122 87 73 53 49 34 121 88 74 54 48 35 0 0 26 15 14 10 87 92 75 80 83 83 1.441 .694 .729 .74 .669 2.295 80 656 .54 .43 110 6830 5010 495 506 677 688 0 101 62 40 .807 102 41 1.239 .848 -.309 -.237
10 2351 822 74 54 2277 768 2532 885 74 55 2458 831 0 0 535 205 13 10 100 100 100 100 3045 3289 2.965 .337 .338 .332 .338 1.174 120 820 .336 .977 120 7220 5010 495 507 716 728 100 956 63 894 .392 1030 967 2.548 .393 -1.35 -1.346
11 656 356 74 54 582 302 661 348 75 54 587 294 0 0 220 121 14 10 100 100 100 100 884 881 1.927 .519 .501 .514 .52 1.226 120 820 .517 .956 120 7600 5010 495 507 754 766 100 414 63 351 .604 405 342 1.656 .583 -.728 -.779
12 2574 1234 74 54 2500 1180 2864 1356 75 55 2790 1302 0 0 845 406 15 10 100 100 100 100 3680 4092 2.119 .472 .467 .474 .477 1.262 156 1140 .47 .978 140 7980 5010 494 508 791 805 100 1436 63 1373 .549 1578 1515 1.821 .543 -.865 -.881
13 345 157 73 54 272 103 340 156 74 55 267 102 0 0 66 29 19 11 100 100 100 100 375 369 2.641 .379 .382 .375 .396 1.398 120 940 .355 .809 130 8340 5030 496 509 827 840 0 183 63 120 .441 181 119 2.27 .444 -1.183 -1.17
14 4104 495 74 53 4030 442 4208 508 75 54 4134 455 0 0 743 86 15 9 100 100 100 100 4472 4589 9.118 .11 .11 .109 .111 1.128 120 940 .107 .972 130 8740 5030 496 509 867 880 100 576 62 514 .128 591 529 7.837 .128 -2.97 -2.965
15 779 121 72 54 707 67 788 118 73 55 716 64 0 0 354 44 16 9 99 97 98 94 774 780 10.552 .095 .089 .093 .094 1.608 208 1512 .09 .773 160 9130 5030 495 511 905 921 100 141 63 78 .11 137 74 9.07 .104 -3.181 -3.265
16 1955 246 72 53 1883 193 1890 246 75 55 1818 193 0 0 330 37 28 23 100 100 100 100 2076 2011 9.756 .102 .106 .102 .1 1.257 156 1272 .098 .839 150 9490 5020 494 509 941 956 100 286 62 225 .119 286 225 8.386 .124 -3.068 -3.017
17 277 133 73 54 204 79 290 136 77 56 217 82 0 0 77 33 37 24 96 93 92 80 283 299 2.582 .387 .378 .388 .381 1.626 208 1512 .401 .714 160 9880 5020 494 510 980 996 100 155 63 92 .451 158 95 2.22 .44 -1.15 -1.186
18 3276 571 73 54 3203 517 3367 579 75 55 3294 525 0 0 599 102 15 9 100 100 100 100 3720 3819 6.195 .161 .159 .161 .161 1.112 120 820 .16 .981 120 10270 5030 497 509 1021 1033 100 664 63 601 .188 674 611 5.325 .185 -2.413 -2.431
19 628 333 73 53 555 280 628 332 75 54 555 279 0 0 201 96 23 11 100 100 99 100 835 834 1.982 .505 .503 .512 .506 1.233 208 1660 .493 .958 170 10650 5030 494 511 1056 1073 100 387 62 326 .587 386 325 1.704 .585 -.769 -.774
20 9697 5334 73 54 9624 5280 10481 5693 75 54 10408 5639 0 0 3295 1647 19 10 100 100 100 100 14904 16047 1.823 .549 .542 .567 .553 1.243 156 1140 .539 .981 140 11020 5000 493 507 1095 1109 100 6206 63 6143 .638 6623 6561 1.567 .63 -.648 -.666

Total number of rows: 24288

Table truncated, full table size 5302 Kbytes.




Supplementary file Size Download File type/resource
GSM498984.gpr.gz 2.0 Mb (ftp)(http) GPR
Processed data included within Sample table
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