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Sample GSM498987 Query DataSets for GSM498987
Status Public on Jan 21, 2010
Title AD4_REP1_LEAF
Sample type RNA
 
Channel 1
Source name AD4 no-salt leaf
Organism Gossypium mustelinum
Characteristics treatment: no-salt
name: 15-c
genome: ad4
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 = AD4 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 = 21 ug; Type of in-vitro transcription = Epicentre; Date performed = Jun-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 = AD4 no-salt leaf; Date performed = 6/8/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura
 
Channel 2
Source name AD4 salt leaf
Organism Gossypium mustelinum
Characteristics treatment: salt
name: 15-c
genome: ad4
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 = AD4 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 = 38 ug; Date performed = Jun-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 = 6/8/2007; Tube label = AD4 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 = 6/11/2007
Scanner Make = Agilent; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 6/11/2007
Description Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58085.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 5582 2614 134 73 5448 2541 6163 2889 135 74 6029 2816 0 0 1612 832 24 13 100 100 100 100 7989 8845 2.144 .466 .467 .461 .466 1.166 120 820 .47 .985 120 3980 3780 372 384 392 404 100 3428 96 3332 .612 3788 3692 1.635 .612 -.709 -.707
2 6522 2818 137 73 6385 2745 4755 2136 152 81 4618 2063 0 0 4533 1956 96 44 100 100 100 99 9130 6681 2.326 .43 .447 .43 .439 1.394 120 940 .422 .939 130 4360 3770 370 383 429 442 100 3695 96 3599 .564 2801 2705 1.774 .586 -.827 -.772
3 16614 9463 135 72 16479 9391 16857 9754 137 73 16722 9682 0 0 4522 2939 25 13 100 100 100 100 25870 26404 1.755 .57 .579 .558 .58 1.199 120 940 .575 .978 130 4730 3780 371 384 466 479 100 12408 94 12314 .747 12790 12695 1.338 .759 -.42 -.397
4 1859 759 135 72 1724 687 1895 799 136 73 1760 727 0 0 550 167 25 13 100 100 100 100 2411 2487 2.509 .398 .413 .41 .405 1.243 120 820 .381 .95 120 5110 3790 373 385 505 517 100 995 94 901 .523 1048 953 1.914 .542 -.936 -.885
5 2855 1958 136 71 2719 1887 3191 2183 137 72 3055 2112 0 0 987 674 23 12 100 100 100 100 4606 5167 1.441 .694 .691 .684 .672 1.361 120 820 .685 .942 120 5490 3800 374 386 543 555 100 2567 93 2474 .91 2862 2769 1.099 .906 -.136 -.142
6 4324 2677 134 74 4190 2603 374 382 136 77 240 308 0 0 5204 3046 26 21 60 100 54 100 6793 548 1.61 .621 1.283 1.632 .639 4.162 392 2816 .595 .991 220 5880 3800 369 391 577 599 100 3510 97 3413 .815 501 404 1.228 1.683 -.296 .751
7 2404 1409 137 72 2267 1337 2471 1453 139 73 2334 1381 0 0 397 337 24 16 100 100 100 100 3604 3715 1.696 .59 .592 .576 .59 1.321 80 656 .601 .929 110 6250 3790 373 384 619 630 100 1847 94 1753 .773 1905 1811 1.293 .776 -.371 -.366
8 501 619 137 72 364 547 503 633 139 72 366 561 0 0 64 104 24 13 100 100 100 100 911 927 .665 1.503 1.533 1.495 1.495 1.229 80 656 1.492 .912 110 6660 3790 373 384 660 671 100 812 94 717 1.97 830 736 .508 2.01 .979 1.007
9 167 118 134 70 33 48 165 118 136 71 31 48 0 0 26 19 25 13 59 98 23 90 81 79 .688 1.455 1.548 1.642 1.389 2.426 52 340 .748 .296 80 7030 3820 378 386 699 707 0 155 92 63 1.907 155 63 .524 2.03 .931 1.022
10 3193 2058 141 72 3052 1986 3163 2072 143 73 3022 2000 0 0 227 205 24 13 100 100 100 100 5038 5022 1.537 .651 .662 .648 .656 1.088 80 656 .642 .96 110 7400 3800 374 385 734 745 100 2698 94 2604 .853 2717 2622 1.172 .868 -.229 -.205
11 890 789 145 73 745 716 915 801 146 74 770 728 0 0 148 171 26 13 100 100 100 100 1461 1498 1.041 .961 .945 .95 .97 1.175 80 656 .965 .959 110 7780 3780 372 383 772 783 100 1035 96 939 1.26 1050 955 .794 1.24 .334 .31
12 14618 9683 157 77 14461 9606 15063 9793 169 91 14906 9716 0 0 1796 1244 120 136 100 100 100 100 24067 24622 1.505 .664 .652 .663 .664 1.104 80 656 .674 .935 110 8170 3780 372 383 811 822 100 12696 101 12595 .871 12841 12740 1.148 .855 -.199 -.227
13 461 368 158 80 303 288 463 370 160 81 305 290 0 0 127 112 28 14 100 100 97 100 591 595 1.052 .95 .951 .962 .977 1.3 120 820 .93 .906 120 8560 3790 373 385 850 862 100 483 105 378 1.246 485 380 .802 1.247 .318 .318
14 10700 4302 168 86 10532 4216 10867 4284 172 88 10699 4198 0 0 934 359 45 39 100 100 100 100 14748 14897 2.498 .4 .392 .4 .401 1.043 80 656 .403 .973 110 8930 3780 372 383 887 898 100 5641 113 5528 .525 5617 5504 1.905 .514 -.93 -.959
15 1738 510 164 84 1574 426 1830 535 167 86 1666 451 0 0 500 156 31 16 100 98 100 98 2000 2117 3.695 .271 .271 .256 .275 1.4 156 1140 .271 .95 140 9300 3790 372 386 923 937 100 669 110 559 .355 701 591 2.818 .355 -1.495 -1.494
16 4774 5211 176 89 4598 5122 5209 5550 177 90 5033 5461 0 0 1620 1423 31 15 100 100 100 100 9720 10494 .898 1.114 1.085 1.198 1.077 1.459 156 1140 1.083 .953 140 9710 3780 371 385 964 978 100 6833 117 6716 1.461 7277 7161 .685 1.423 .547 .509
17 346 233 181 90 165 143 320 222 182 92 139 132 0 0 127 58 35 16 99 100 95 99 308 271 1.154 .867 .95 .929 .94 1.573 120 940 .629 .658 130 10070 3790 372 385 1000 1013 100 306 118 188 1.136 291 173 .88 1.245 .184 .316
18 10107 3667 192 96 9915 3571 11443 4240 195 96 11251 4144 0 0 3593 1394 33 18 100 100 100 100 13486 15395 2.777 .36 .368 .357 .375 1.24 120 820 .362 .979 120 10480 3780 372 384 1042 1054 100 4808 126 4682 .472 5560 5434 2.118 .483 -1.082 -1.05
19 2507 1424 195 96 2312 1328 2321 1387 197 98 2126 1291 0 0 694 435 37 17 100 100 100 100 3640 3417 1.741 .574 .607 .557 .594 1.372 156 1140 .569 .945 140 10810 3800 373 387 1074 1088 100 1867 126 1741 .753 1819 1693 1.328 .796 -.409 -.329
20 22884 17034 205 100 22679 16934 23961 18651 206 101 23756 18551 0 0 5325 4848 34 18 100 100 100 100 39613 42307 1.339 .747 .781 .724 .772 1.256 120 820 .757 .98 120 11230 3780 372 384 1117 1129 100 22335 131 22204 .979 24455 24324 1.021 1.024 -.031 .034

Total number of rows: 24288

Table truncated, full table size 5507 Kbytes.




Supplementary file Size Download File type/resource
GSM498987.gpr.gz 2.1 Mb (ftp)(http) GPR
Processed data included within Sample table
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