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Sample GSM498978 Query DataSets for GSM498978
Status Public on Jan 21, 2010
Title AD1_REP2_LEAF
Sample type RNA
 
Channel 1
Source name AD1 no-salt leaf
Organism Gossypium hirsutum
Characteristics treatment: no-salt
name: tm1
genome: ad1
polyploid level: 4x
tissue type: leaf
Treatment protocol BYU growth chamber
Extracted molecule total RNA
Extraction protocol Date performed = May-07; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD1 no-salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"
Label Cy3
Label protocol Approx RNA yield = 16 ug; Type of in-vitro transcription = Epicentre; Date performed = Sep-07; 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 leaf; Date performed = 9/5/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura
 
Channel 2
Source name AD1 salt leaf
Organism Gossypium hirsutum
Characteristics treatment: salt
name: tm1
genome: ad1
tissue type: leaf
polyploid level: 4x
Treatment protocol BYU growth chamber
Extracted molecule total RNA
Extraction protocol Date performed = May-07; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD1 salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"; Name = Rozaura; Extracted molecule = RNA
Label Cy5
Label protocol Approx RNA yield = 15.5 ug; Date performed = Sep-07; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 9/5/2007; Tube label = AD1 salt leaf; 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 = 9/12/2007
Scanner Make = Agilent; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 9/12/2007
Description Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58065.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 2620 3268 142 91 2478 3177 2682 3290 171 110 2540 3199 0 0 643 756 172 107 100 100 100 100 5655 5739 .78 1.282 1.259 1.29 1.308 1.23 120 940 1.259 .92 130 3800 4800 473 486 373 386 100 2258 63 2195 .886 2273 2211 1.129 .87 -.175 -.2
2 1774 1575 134 86 1640 1489 1474 1262 137 89 1340 1176 0 0 1062 986 37 25 100 100 100 100 3129 2516 1.101 .908 .878 .914 .914 1.212 120 940 .915 .965 130 4190 4810 474 487 412 425 100 1088 59 1029 .627 872 813 1.594 .606 -.673 -.722
3 4548 4692 143 91 4405 4601 4555 4682 146 93 4412 4591 0 0 868 932 29 19 100 100 100 100 9006 9003 .957 1.044 1.041 1.048 1.05 1.147 120 940 1.03 .971 130 4570 4810 474 487 450 463 100 3242 63 3179 .722 3235 3173 1.385 .719 -.47 -.476
4 533 566 141 93 392 473 532 575 145 95 391 482 0 0 95 103 32 23 99 100 99 99 865 873 .829 1.207 1.233 1.209 1.214 1.195 120 940 1.193 .917 130 4960 4810 474 487 489 502 100 391 64 327 .834 397 333 1.199 .852 -.262 -.231
5 1625 1514 140 88 1485 1426 1656 1573 141 90 1516 1485 0 0 321 330 28 20 100 100 100 100 2911 3001 1.041 .96 .98 .951 .966 1.184 120 820 .959 .975 120 5330 4810 475 487 527 539 100 1046 61 985 .664 1087 1026 1.507 .677 -.592 -.563
6 2373 1985 144 94 2229 1891 484 659 146 99 340 565 0 0 2604 1927 29 28 56 100 54 100 4120 905 1.179 .848 1.662 1.559 .825 3.83 392 2788 .773 .966 220 5740 4830 472 494 563 585 100 1372 65 1307 .586 455 390 1.706 1.148 -.77 .2
7 2141 3155 143 90 1998 3065 2274 3284 145 91 2131 3194 0 0 632 1147 25 17 100 100 100 100 5063 5325 .652 1.534 1.499 1.506 1.542 1.286 120 820 1.577 .968 120 6110 4800 474 486 605 617 100 2180 62 2118 1.06 2269 2207 .943 1.036 .084 .051
8 512 768 145 92 367 676 535 836 151 95 390 744 0 0 119 224 63 32 96 100 95 100 1043 1134 .543 1.842 1.908 1.862 1.809 1.453 120 820 1.854 .928 120 6480 4830 477 489 642 654 100 531 64 467 1.273 578 514 .786 1.318 .348 .399
9 201 221 139 85 62 136 193 220 140 86 54 135 0 0 42 43 31 19 75 100 46 100 198 189 .456 2.194 2.5 2.926 2.409 2.708 52 420 .996 .346 90 6860 4840 479 488 681 690 0 153 59 94 1.516 152 93 .66 1.728 .6 .789
10 444 421 142 92 302 329 449 442 144 94 307 350 0 0 114 119 26 17 98 99 95 98 631 657 .918 1.089 1.14 1.094 1.103 1.458 120 820 1.076 .895 120 7240 4790 473 485 718 730 100 291 64 227 .753 305 242 1.328 .788 -.41 -.344
11 509 695 139 90 370 605 502 709 141 92 363 619 0 0 168 262 29 21 97 100 95 100 975 982 .612 1.635 1.705 1.679 1.629 1.383 120 820 1.622 .94 120 7640 4800 474 486 758 770 100 480 62 418 1.13 490 428 .885 1.178 .176 .237
12 2583 2530 141 91 2442 2439 2623 2592 143 92 2482 2501 0 0 482 446 26 18 100 100 100 100 4881 4983 1.001 .999 1.008 1 .997 1.134 120 820 .997 .981 120 8020 4800 474 486 796 808 100 1748 63 1685 .69 1791 1728 1.449 .696 -.535 -.522
13 816 698 141 93 675 605 775 686 143 95 634 593 0 0 321 235 25 25 100 100 100 100 1280 1227 1.116 .896 .935 .901 .929 1.2 120 820 .858 .927 120 8400 4800 474 486 834 846 100 482 64 418 .619 474 410 1.615 .646 -.691 -.63
14 2607 2556 142 92 2465 2464 2596 2535 147 94 2454 2443 0 0 550 466 38 23 100 100 100 100 4929 4897 1 1 .996 1.011 1.007 1.178 120 820 .987 .971 120 8780 4800 474 486 872 884 100 1766 64 1703 .691 1752 1688 1.448 .688 -.534 -.54
15 445 440 142 93 303 347 433 425 146 97 291 332 0 0 98 87 37 31 100 100 100 100 650 623 .873 1.145 1.141 1.167 1.173 1.33 156 1272 1.085 .864 150 9180 4800 472 487 910 925 100 304 64 240 .791 294 229 1.264 .788 -.338 -.343
16 2202 1952 145 91 2057 1861 2157 1949 147 92 2012 1858 0 0 527 382 28 17 100 100 100 100 3918 3870 1.105 .905 .923 .918 .937 1.191 156 1140 .883 .956 140 9550 4800 473 487 948 962 100 1349 63 1286 .625 1347 1284 1.6 .638 -.678 -.648
17 407 462 141 90 266 372 409 473 144 92 268 383 0 0 73 83 26 18 100 100 100 100 638 651 .715 1.398 1.429 1.42 1.44 1.257 120 940 1.331 .893 130 9940 4810 474 487 987 1000 100 319 62 257 .966 327 265 1.035 .988 -.049 -.018
18 1929 1739 145 95 1784 1644 2118 1814 149 97 1973 1719 0 0 630 462 28 24 100 100 100 100 3428 3692 1.085 .922 .871 1.003 .918 1.446 120 820 .892 .96 120 10310 4790 473 485 1025 1037 100 1202 66 1136 .637 1254 1188 1.57 .602 -.651 -.732
19 1188 1187 146 93 1042 1094 877 789 176 119 731 696 0 0 1269 1322 324 306 87 91 62 61 2136 1427 .952 1.05 .952 1.075 1.019 1.522 208 1660 1.022 .959 170 10690 4790 470 487 1060 1077 100 820 64 756 .726 545 481 1.378 .658 -.463 -.604
20 6607 6769 150 92 6457 6677 6591 6884 153 94 6441 6792 0 0 901 1025 33 17 100 100 100 100 13134 13233 .967 1.034 1.054 1.03 1.05 1.125 120 820 1.04 .975 120 11080 4780 472 484 1102 1114 100 4678 64 4614 .715 4757 4693 1.399 .729 -.485 -.457

Total number of rows: 24288

Table truncated, full table size 5517 Kbytes.




Supplementary file Size Download File type/resource
GSM498978.gpr.gz 2.1 Mb (ftp)(http) GPR
Processed data included within Sample table
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