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Sample GSM498974 Query DataSets for GSM498974
Status Public on Jan 21, 2010
Title AD5_REP3_ROOT
Sample type RNA
 
Channel 1
Source name AD5 salt root
Organism Gossypium darwinii
Characteristics treatment: salt
name: pw45
genome: ad5
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 = AD5 salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = root tissue
Label Cy3
Label protocol Approx RNA yield = 11 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 = AD5 salt root; Date performed = 3/31/2008; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura
 
Channel 2
Source name AD5 no-salt root
Organism Gossypium darwinii
Characteristics treatment: no-salt
name: pw45
genome: ad5
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 = AD5 no-salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = root tissue; Name = Rozaura; Extracted molecule = RNA
Label Cy5
Label protocol Approx RNA yield = 19 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 = AD5 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//58098.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 1379 2252 84 238 1295 2014 1406 2314 85 254 1322 2076 0 0 340 494 14 80 100 100 100 100 3309 3398 .643 1.555 1.57 1.566 1.529 1.211 120 940 1.544 .925 130 4180 5480 541 554 411 424 100 1420 150 1270 .981 1459 1309 1.019 .99 -.028 -.014
2 235 639 93 298 142 341 218 624 105 374 125 326 0 0 61 161 37 187 100 78 93 37 483 451 .416 2.401 2.608 2.342 2.62 2.03 32 236 5.311 .248 70 4590 5510 547 554 455 462 0 403 188 215 1.515 394 206 .66 1.645 .599 .718
3 6348 9502 85 296 6263 9206 6509 9630 86 330 6424 9334 0 0 1045 1405 16 157 100 100 100 100 15469 15758 .68 1.47 1.453 1.475 1.465 1.101 120 940 1.464 .977 130 4950 5490 542 555 488 501 100 5993 187 5806 .927 6074 5887 1.079 .916 -.109 -.126
4 561 1251 87 438 474 813 608 1160 87 394 521 722 0 0 168 309 14 178 99 99 97 97 1287 1243 .583 1.715 1.386 1.765 1.525 2.066 156 1140 2.433 .52 140 5330 5500 543 557 526 540 100 789 276 513 1.082 732 455 .924 .874 .113 -.194
5 252 1695 88 530 164 1165 251 1648 90 548 163 1118 0 0 55 328 16 203 100 100 99 98 1329 1281 .141 7.104 6.859 7.316 7.18 1.463 120 820 7.889 .688 120 5700 5490 543 555 564 576 100 1069 334 735 4.48 1039 705 .223 4.326 2.164 2.113
6 607 2227 90 580 517 1647 616 2241 95 605 526 1661 0 0 86 272 74 189 100 100 100 100 2164 2187 .314 3.186 3.158 3.185 3.204 1.243 156 1272 3.235 .737 150 6100 5500 542 557 602 617 100 1405 366 1039 2.009 1413 1048 .498 1.992 1.007 .994
7 606 1835 90 549 516 1286 620 1835 91 551 530 1286 0 0 120 226 15 137 100 100 100 100 1802 1816 .401 2.492 2.426 2.534 2.41 1.324 120 940 2.615 .803 130 6490 5490 542 555 642 655 100 1157 346 811 1.572 1157 811 .636 1.53 .652 .614
8 919 3491 88 515 831 2976 962 3523 90 522 874 3008 0 0 184 533 16 196 100 100 100 100 3807 3882 .279 3.581 3.442 3.634 3.539 1.232 120 940 3.656 .92 130 6860 5490 542 555 679 692 100 2202 325 1877 2.259 2222 1897 .443 2.171 1.175 1.118
9 116 834 89 475 27 359 117 723 91 507 28 248 0 0 24 468 17 152 62 58 37 47 386 276 .075 13.296 8.857 17.654 21.214 3.938 156 1140 39.342 .135 140 7240 5480 541 555 717 731 0 526 300 226 8.386 456 156 .119 5.586 3.068 2.482
10 3153 3406 91 494 3062 2912 3271 3397 92 530 3180 2903 0 0 602 498 17 165 100 100 100 100 5974 6083 1.052 .951 .913 .962 .928 1.189 120 940 .951 .92 130 7620 5480 541 554 755 768 100 2148 312 1837 .6 2142 1831 1.667 .576 -.737 -.796
11 319 1543 92 497 227 1046 233 1697 92 533 141 1200 0 0 230 504 16 158 72 94 66 89 1273 1341 .217 4.608 8.511 8.437 5.343 3.53 208 1512 4.271 .613 160 8010 5490 541 557 793 809 100 973 313 660 2.906 1070 757 .344 5.368 1.539 2.424
12 8249 3308 90 506 8159 2802 8779 3556 93 550 8689 3050 0 0 2317 811 22 247 100 99 100 99 10961 11739 2.912 .343 .351 .343 .339 1.229 120 940 .341 .93 130 8390 5470 540 553 832 845 100 2086 319 1767 .217 2243 1924 4.617 .221 -2.207 -2.175
13 201 1241 91 536 110 705 211 1282 93 580 120 746 0 0 48 330 19 174 91 91 89 85 815 866 .156 6.409 6.217 6.537 6.49 3.071 156 1272 10.47 .428 150 8760 5500 542 557 868 883 100 783 338 445 4.042 809 471 .247 3.921 2.015 1.971
14 3923 3126 89 462 3834 2664 4368 3233 90 512 4279 2771 0 0 1444 842 17 175 100 100 99 100 6498 7050 1.439 .695 .648 .776 .68 1.748 156 1140 .647 .913 140 9150 5480 541 555 908 922 100 1972 291 1680 .438 2039 1748 2.282 .408 -1.19 -1.292
15 677 1293 90 532 587 761 715 1233 92 580 625 701 0 0 233 451 29 279 99 80 96 62 1348 1326 .771 1.296 1.122 1.167 1.29 2.707 208 1512 1.742 .497 160 9540 5490 541 557 946 962 100 815 336 480 .818 778 442 1.223 .707 -.29 -.499
16 672 1455 93 607 579 848 677 1478 94 651 584 871 0 0 141 215 20 474 100 95 100 33 1427 1455 .683 1.465 1.491 1.458 1.457 1.364 156 1140 1.612 .767 140 9920 5490 542 556 985 999 100 918 383 535 .924 932 549 1.083 .941 -.114 -.088
17 283 1025 90 545 193 480 302 940 91 602 212 395 0 0 117 462 18 386 89 50 82 29 673 607 .402 2.487 1.863 2.632 2.884 6.368 256 1924 7.247 .184 180 10300 5500 541 559 1021 1039 100 646 344 303 1.569 593 249 .638 1.175 .649 .233
18 4159 5057 89 542 4070 4515 4529 5198 92 583 4440 4656 0 0 1106 906 27 202 100 100 100 100 8585 9096 .901 1.109 1.049 1.15 1.062 1.311 120 820 1.054 .942 120 10680 5470 541 553 1062 1074 100 3189 342 2848 .7 3278 2937 1.429 .661 -.515 -.596
19 978 1485 89 539 889 946 1016 1419 98 591 927 880 0 0 257 351 54 223 100 100 98 100 1835 1807 .94 1.064 .949 1.083 .902 1.931 208 1660 1.246 .557 170 11070 5500 541 558 1098 1115 100 937 340 597 .671 895 555 1.49 .599 -.575 -.74
20 17153 14778 91 575 17062 14203 17352 14934 94 625 17261 14359 0 0 2126 1572 20 213 100 100 100 100 31265 31620 1.201 .832 .832 .835 .824 1.083 120 940 .823 .982 130 11440 5480 541 554 1137 1150 100 9321 363 8958 .525 9419 9056 1.905 .525 -.93 -.931

Total number of rows: 24288

Table truncated, full table size 5469 Kbytes.




Supplementary file Size Download File type/resource
GSM498974.gpr.gz 2.1 Mb (ftp)(http) GPR
Processed data included within Sample table
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