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Sample GSM498981 Query DataSets for GSM498981
Status Public on Jan 21, 2010
Title AD3_REP2_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 = 10/29/2007; 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 3 plants"
Label Cy3
Label protocol Approx RNA yield = 8 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 = AD3 no-salt root; Date performed = 2/18/2008; 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 = 10/29/2007; 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 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 = 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 = 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//58082.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 1270 961 93 89 1177 872 1222 846 128 112 1129 757 0 0 784 613 234 158 86 87 74 76 2049 1886 1.35 .741 .671 .767 .737 1.417 156 1272 .737 .97 150 3970 3930 385 400 389 404 100 783 73 711 .604 689 617 1.656 .546 -.728 -.872
2 422 310 94 91 328 219 389 286 99 96 295 195 0 0 168 121 38 29 99 100 96 100 547 490 1.498 .668 .661 .671 .657 1.393 120 820 .644 .886 120 4300 3920 386 398 424 436 100 253 74 178 .544 233 159 1.838 .539 -.878 -.893
3 2904 2652 97 96 2807 2556 2458 2136 118 113 2361 2040 0 0 2601 2360 91 74 83 86 78 81 5363 4401 1.098 .911 .864 1.025 .918 1.779 392 2706 .908 .993 220 4660 3950 384 406 455 477 100 2161 78 2083 .742 1741 1662 1.348 .704 -.431 -.506
4 1140 947 98 101 1042 846 1237 995 111 241 1139 894 0 0 757 613 53 2068 94 5 87 0 1888 2033 1.232 .812 .785 .866 .813 1.45 156 1140 22.697 .036 140 5020 3930 386 400 495 509 0 772 82 689 .662 811 728 1.512 .64 -.596 -.645
5 409 340 99 100 310 240 343 303 111 140 244 203 0 0 324 218 68 907 89 1 80 0 550 447 1.292 .774 .832 .818 .789 1.634 256 2004 .698 .875 190 5390 3920 382 401 529 548 0 277 81 196 .631 247 165 1.585 .678 -.665 -.561
6 1196 882 97 103 1099 779 259 258 103 120 162 155 0 0 1412 940 42 227 68 43 58 37 1878 317 1.411 .709 .957 1.21 .823 2.695 460 3058 .703 .847 240 5750 3950 383 407 563 587 0 719 84 635 .578 210 126 1.731 .78 -.792 -.359
7 721 839 97 101 624 738 661 785 103 119 564 684 0 0 484 544 31 277 91 68 87 58 1362 1248 .846 1.183 1.213 1.315 1.178 1.677 256 1924 1.159 .973 180 6160 3930 384 402 607 625 100 684 82 601 .964 640 557 1.038 .988 -.053 -.017
8 1701 2620 100 107 1601 2513 2056 3237 106 114 1956 3130 0 0 1330 1980 33 33 85 97 76 89 4114 5086 .637 1.57 1.6 1.936 1.587 1.862 256 1916 1.532 .989 180 6550 3920 383 401 646 664 100 2135 87 2048 1.279 2638 2551 .782 1.304 .355 .383
9 170 278 100 113 70 165 169 283 158 119 69 170 0 0 42 72 1313 32 0 98 0 90 235 239 .424 2.357 2.464 2.444 2.306 2.055 256 1916 2.191 .498 180 6920 3910 382 400 683 701 0 227 92 134 1.921 231 139 .521 2.008 .942 1.005
10 2229 1891 104 117 2125 1774 2658 2243 115 120 2554 2126 0 0 1101 826 65 26 99 100 97 100 3899 4680 1.198 .835 .832 .89 .827 1.307 120 940 .812 .979 130 7330 3920 385 398 726 739 100 1541 95 1446 .68 1828 1732 1.47 .678 -.556 -.56
11 967 1363 104 113 863 1250 1017 1523 111 118 913 1410 0 0 422 601 38 33 100 100 99 100 2113 2323 .69 1.448 1.544 1.461 1.444 1.191 208 1660 1.448 .979 170 7680 3920 383 400 759 776 100 1111 92 1019 1.18 1241 1149 .847 1.258 .239 .332
12 20108 7801 101 95 20007 7706 15782 6332 121 104 15681 6237 0 0 18876 7118 87 43 92 95 88 89 27713 21918 2.596 .385 .398 .468 .392 1.734 208 1512 .378 .984 160 8090 3920 384 400 801 817 100 6357 77 6279 .314 5160 5082 3.186 .324 -1.672 -1.625
13 319 274 96 88 223 186 295 264 103 92 199 176 0 0 256 135 39 24 89 95 81 90 409 375 1.199 .834 .884 .974 .876 1.981 316 2321 .623 .818 200 8460 3930 383 403 836 856 0 223 72 152 .68 215 143 1.471 .721 -.557 -.473
14 1894 1363 92 83 1802 1280 690 619 98 87 598 536 0 0 1951 1316 31 25 82 89 73 80 3082 1134 1.408 .71 .896 .955 .737 1.939 256 1772 .687 .989 180 8850 3930 384 402 876 894 100 1111 68 1043 .579 504 437 1.728 .73 -.789 -.453
15 422 307 93 82 329 225 246 202 101 88 153 120 0 0 345 213 50 34 69 81 57 63 554 273 1.462 .684 .784 .812 .725 1.994 460 3206 .636 .933 250 9170 3930 380 405 904 929 0 250 67 183 .557 165 98 1.794 .639 -.844 -.646
16 4494 1207 100 85 4394 1122 5443 1424 148 101 5343 1339 0 0 2232 558 200 66 95 97 92 94 5516 6682 3.916 .255 .251 .273 .255 1.426 208 1512 .25 .979 160 9580 3910 383 399 950 966 100 984 69 914 .208 1160 1091 4.806 .204 -2.265 -2.292
17 336 286 95 78 241 208 352 285 102 82 257 207 0 0 178 139 37 23 83 98 73 91 449 464 1.159 .863 .805 1.053 .886 2.02 208 1512 .807 .888 160 9960 3930 385 401 988 1004 100 233 64 169 .703 232 169 1.422 .656 -.508 -.608
18 2200 1624 96 78 2104 1546 428 329 106 84 332 251 0 0 2726 1983 65 35 70 91 62 73 3650 583 1.361 .735 .756 .935 .781 1.953 256 1918 .728 .991 180 10370 3930 384 402 1028 1046 100 1323 64 1260 .599 268 205 1.67 .616 -.74 -.699
19 1613 1208 103 83 1510 1125 1611 1268 117 94 1508 1185 0 0 809 483 64 45 100 100 99 100 2635 2693 1.342 .745 .786 .777 .762 1.225 156 1272 .709 .946 150 10720 3920 384 399 1064 1079 100 984 68 917 .607 1033 966 1.647 .64 -.72 -.643
20 7985 6134 101 83 7884 6051 6422 5413 235 181 6321 5330 0 0 7430 5411 1387 986 62 66 58 62 13935 11651 1.303 .768 .843 .887 .781 1.917 256 2064 .737 .967 190 11140 3920 382 401 1104 1123 100 4998 68 4931 .625 4411 4343 1.599 .687 -.677 -.541

Total number of rows: 24288

Table truncated, full table size 5488 Kbytes.




Supplementary file Size Download File type/resource
GSM498981.gpr.gz 2.2 Mb (ftp)(http) GPR
Processed data included within Sample table
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