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Sample GSM498992 Query DataSets for GSM498992
Status Public on Jan 21, 2010
Title AD1_REP4_ROOT
Sample type RNA
 
Channel 1
Source name AD1 no-salt root
Organism Gossypium hirsutum
Characteristics treatment: no-salt
name: tm1
genome: ad1
polyploid level: 4x
tissue type: root
Treatment protocol BYU growth chamber
Extracted molecule total RNA
Extraction protocol Date performed = 10/10/2007; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD1 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 = 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 = AD1 no-salt root; Date performed = 11/29/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura
 
Channel 2
Source name AD1 salt root
Organism Gossypium hirsutum
Characteristics treatment: salt
name: tm1
genome: ad1
tissue type: root
polyploid level: 4x
Treatment protocol BYU growth chamber
Extracted molecule total RNA
Extraction protocol Date performed = 10/10/2007; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD1 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 = 16 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 = AD1 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//58070.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 3780 4229 113 118 3667 4111 4020 4523 237 151 3907 4405 0 0 922 1007 1249 206 95 100 86 100 7778 8312 .892 1.121 1.127 1.128 1.125 1.116 120 820 1.114 .985 120 4290 5310 525 537 423 435 100 2385 67 2318 .632 2550 2484 1.582 .636 -.662 -.653
2 358 272 125 123 233 149 224 211 229 179 99 88 0 0 455 212 486 249 13 18 7 7 382 187 1.564 .639 .889 .828 .883 2.43 256 2050 .48 .904 190 4700 5320 522 541 460 479 0 153 69 84 .361 119 50 2.773 .501 -1.472 -.996
3 4368 4436 167 151 4201 4285 1086 727 329 230 919 576 0 0 5502 5880 643 290 56 61 43 50 8486 1495 .98 1.02 .627 .765 .92 2.017 392 2703 1.043 .964 230 5080 5330 521 544 496 519 100 2501 85 2416 .575 410 325 1.739 .353 -.798 -1.501
4 1126 1077 221 186 905 891 1174 954 481 310 953 768 0 0 917 765 913 418 51 57 5 49 1796 1721 1.016 .985 .806 .852 1.032 1.901 256 2007 .619 .643 190 5440 5290 519 538 534 553 100 607 105 502 .555 538 433 1.801 .454 -.849 -1.138
5 1064 834 251 261 813 573 438 460 505 380 187 199 0 0 1877 823 817 397 25 42 13 31 1386 386 1.419 .705 1.064 .892 .808 2.342 316 2314 .434 .733 200 5820 5300 520 540 572 592 100 470 147 323 .397 259 112 2.516 .6 -1.331 -.737
6 2336 2816 134 222 2202 2594 2450 2907 464 362 2316 2685 0 0 634 575 1355 442 89 100 16 98 4796 5001 .849 1.178 1.159 1.222 1.172 1.337 156 1272 1.097 .922 150 6170 5330 525 540 609 624 100 1588 125 1463 .664 1639 1514 1.505 .654 -.59 -.613
7 2063 2723 126 132 1937 2591 2067 2769 128 137 1941 2637 0 0 663 745 25 32 100 100 100 100 4528 4578 .748 1.338 1.359 1.335 1.394 1.252 120 820 1.32 .917 120 6600 5320 526 538 654 666 100 1535 74 1461 .754 1561 1487 1.326 .766 -.407 -.384
8 3493 3459 128 139 3365 3320 3725 4165 151 155 3597 4026 0 0 2682 2025 176 84 90 94 89 91 6685 7623 1.014 .987 1.119 1 1.087 1.672 156 1140 .877 .828 140 6980 5310 524 538 691 705 100 1950 78 1872 .556 2349 2270 1.797 .631 -.846 -.664
9 804 1121 127 140 677 981 740 1026 132 147 613 886 0 0 345 420 42 45 100 100 100 100 1658 1499 .69 1.449 1.445 1.507 1.486 1.279 80 656 1.394 .933 110 7350 5310 525 536 729 740 100 632 79 553 .817 579 500 1.224 .815 -.291 -.295
10 3453 3537 121 134 3332 3403 3787 3839 132 146 3666 3705 0 0 1286 1226 86 84 100 100 98 100 6735 7371 .979 1.021 1.011 1.065 1.038 1.303 120 820 1.01 .976 120 7730 5310 525 537 767 779 100 1994 76 1919 .576 2165 2089 1.736 .57 -.796 -.811
11 1311 1964 119 116 1192 1848 1344 2150 124 123 1225 2034 0 0 574 846 37 45 98 100 96 99 3040 3259 .645 1.55 1.66 1.599 1.658 1.354 120 820 1.544 .945 120 8110 5310 525 537 805 817 100 1107 65 1042 .874 1212 1147 1.144 .936 -.194 -.095
12 10879 7546 121 115 10758 7431 11676 8045 140 124 11555 7930 0 0 3134 2506 191 49 100 100 100 100 18189 19485 1.448 .691 .686 .667 .699 1.235 120 940 .701 .974 130 8500 5290 522 535 843 856 100 4255 65 4190 .389 4536 4471 2.567 .387 -1.36 -1.37
13 715 953 119 120 596 833 686 969 146 137 567 849 0 0 235 193 276 110 94 100 54 100 1429 1416 .715 1.398 1.497 1.467 1.526 1.345 120 940 1.269 .838 130 8890 5310 524 537 882 895 100 537 68 470 .788 546 479 1.269 .844 -.344 -.244
14 4161 4193 113 114 4048 4079 4079 4173 115 126 3966 4059 0 0 779 820 23 70 100 100 100 100 8127 8025 .992 1.008 1.023 1.005 1.017 1.108 120 820 1.012 .981 120 9280 5300 524 536 922 934 100 2364 64 2300 .568 2353 2289 1.76 .577 -.816 -.793
15 935 1150 118 119 817 1031 947 1162 127 129 829 1043 0 0 159 179 48 53 100 100 100 100 1848 1872 .792 1.262 1.258 1.267 1.288 1.198 156 1272 1.257 .946 150 9660 5310 523 538 958 973 100 648 67 581 .712 655 588 1.405 .709 -.491 -.495
16 1085 1339 158 143 927 1196 1114 1438 228 188 956 1295 0 0 227 339 292 194 98 97 92 94 2123 2251 .775 1.29 1.355 1.248 1.285 1.264 156 1272 1.322 .927 150 10040 5290 521 536 996 1011 100 755 81 674 .727 811 730 1.375 .764 -.459 -.389
17 406 668 152 135 254 533 437 850 191 157 285 715 0 0 141 380 166 91 72 75 33 68 787 1000 .477 2.098 2.509 1.578 2.269 2.528 256 1924 2.478 .636 180 10410 5290 520 538 1032 1050 100 377 76 301 1.183 479 403 .845 1.415 .243 .5
18 4963 4274 118 119 4845 4155 5453 4912 142 137 5335 4793 0 0 1625 1637 169 86 100 100 100 100 9000 10128 1.166 .858 .898 .814 .887 1.308 120 940 .878 .972 130 10810 5290 522 535 1074 1087 100 2410 67 2343 .484 2770 2703 2.068 .507 -1.048 -.981
19 1493 1450 125 121 1368 1329 1427 1435 204 159 1302 1314 0 0 291 239 429 172 100 100 98 100 2697 2616 1.029 .971 1.009 .975 .983 1.119 156 1272 .737 .75 150 11180 5300 522 537 1110 1125 100 818 68 749 .548 809 741 1.825 .569 -.868 -.813
20 10061 10400 129 124 9932 10276 12983 13181 222 172 12854 13057 0 0 7857 7999 563 238 75 82 72 77 20208 25911 .967 1.035 1.016 1.118 1.029 2.517 208 1512 1.027 .979 160 11570 5280 520 536 1149 1165 100 5864 70 5794 .583 7432 7362 1.714 .573 -.777 -.804

Total number of rows: 24288

Table truncated, full table size 5660 Kbytes.




Supplementary file Size Download File type/resource
GSM498992.gpr.gz 2.2 Mb (ftp)(http) GPR
Processed data included within Sample table
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