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Sample GSM498980 Query DataSets for GSM498980
Status Public on Jan 21, 2010
Title AD1_REP2_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 = 10/25/2007; 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 = 7 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 = AD1 no-salt root; Date performed = 2/18/2008; 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 = 10/25/2007; 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 = 9 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 = 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 = 2/22/2007
Scanner Make = Agilent; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 2/22/2007
Description Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58066.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 3420 2733 77 61 3343 2672 3800 3005 78 63 3723 2944 0 0 994 712 17 16 100 100 100 100 6015 6667 1.251 .799 .791 .822 .786 1.274 120 820 .79 .985 120 4040 4680 462 474 398 410 100 1868 42 1827 .546 2054 2013 1.83 .541 -.872 -.887
2 158 171 74 59 84 112 158 162 76 61 84 103 0 0 44 55 17 16 93 97 88 93 196 187 .75 1.333 1.226 1.386 1.343 1.512 80 656 .216 .108 110 4420 4700 464 475 436 447 0 117 40 77 .912 111 70 1.097 .838 -.134 -.254
3 7893 8241 78 63 7815 8178 7975 8447 96 66 7897 8384 0 0 1091 1321 293 27 100 100 100 100 15993 16281 .956 1.046 1.062 1.042 1.055 1.096 120 940 1.048 .977 130 4810 4680 461 474 474 487 100 5634 43 5591 .715 5775 5732 1.398 .726 -.483 -.462
4 903 792 76 61 827 731 930 814 78 62 854 753 0 0 153 142 20 13 100 100 100 100 1558 1607 1.131 .884 .882 .879 .897 1.135 120 820 .886 .979 120 5170 4690 463 475 511 523 100 541 42 500 .604 557 515 1.655 .603 -.727 -.73
5 309 353 77 63 232 290 321 372 79 65 244 309 0 0 100 107 20 22 99 100 96 96 522 553 .8 1.25 1.266 1.255 1.264 1.349 120 820 1.23 .909 120 5570 4700 464 476 551 563 100 241 43 198 .855 254 211 1.17 .866 -.227 -.208
6 1057 831 78 66 979 765 96 402 80 69 18 336 0 0 1283 691 25 20 47 100 44 100 1744 354 1.28 .781 18.667 2.762 .801 6.464 460 3198 .61 .948 240 5950 4710 459 483 583 607 0 568 45 523 .534 275 230 1.872 12.762 -.904 3.674
7 1623 1491 76 64 1547 1427 1777 1621 78 66 1701 1557 0 0 433 485 16 20 100 100 100 100 2974 3258 1.084 .922 .915 .887 .936 1.252 120 820 .942 .977 120 6340 4700 464 476 628 640 100 1019 44 976 .631 1108 1064 1.586 .626 -.665 -.676
8 2261 1734 79 68 2182 1666 2750 2092 80 69 2671 2024 0 0 983 729 15 13 96 96 96 96 3848 4695 1.31 .764 .758 .778 .765 1.507 156 1140 .759 .984 140 6720 4700 463 477 665 679 100 1186 46 1139 .522 1430 1384 1.916 .518 -.938 -.949
9 154 201 77 66 77 135 139 183 79 68 62 117 0 0 77 96 17 17 100 100 88 98 212 179 .57 1.753 1.887 1.863 1.869 1.592 80 560 1.588 .721 100 7100 4690 464 474 705 715 0 137 45 92 1.199 125 80 .834 1.29 .261 .368
10 2357 3387 81 74 2276 3313 2579 3702 98 77 2498 3628 0 0 690 930 237 30 99 100 96 100 5589 6126 .687 1.456 1.452 1.483 1.452 1.184 120 940 1.429 .923 130 7490 4680 461 474 742 755 100 2316 51 2265 .995 2531 2480 1.005 .993 -.007 -.01
11 815 1976 79 69 736 1907 788 1985 87 94 709 1916 0 0 209 528 140 457 100 100 100 97 2643 2625 .386 2.591 2.702 2.592 2.59 1.175 80 656 3.576 .928 110 7890 4700 464 475 783 794 100 1351 47 1304 1.771 1357 1310 .565 1.848 .825 .886
12 14141 7186 82 71 14059 7115 15046 7572 93 77 14964 7501 0 0 3051 1510 110 77 100 100 100 100 21174 22465 1.976 .506 .501 .509 .505 1.132 120 820 .504 .989 120 8250 4700 464 476 819 831 100 4913 49 4864 .346 5177 5128 2.89 .343 -1.531 -1.545
13 272 349 80 71 192 278 276 354 83 72 196 283 0 0 59 69 20 16 99 100 98 99 470 479 .691 1.448 1.444 1.471 1.475 1.345 120 940 1.428 .895 130 8610 4710 464 477 854 867 100 239 49 190 .99 242 193 1.01 .987 -.015 -.019
14 4550 4060 82 70 4468 3990 4675 4264 86 73 4593 4194 0 0 777 1025 23 20 100 100 100 100 8458 8787 1.12 .893 .913 .863 .921 1.33 120 820 .913 .961 120 9020 4710 465 477 896 908 100 2776 48 2728 .611 2915 2867 1.638 .624 -.712 -.68
15 1055 934 80 66 975 868 1051 938 87 69 971 872 0 0 169 136 90 39 100 100 100 100 1843 1843 1.123 .89 .898 .894 .894 1.118 156 1272 .885 .968 150 9410 4690 461 476 933 948 100 639 45 593 .609 641 596 1.643 .614 -.716 -.704
16 674 938 80 66 594 872 705 998 83 68 625 932 0 0 149 232 30 20 100 100 99 100 1466 1557 .681 1.468 1.491 1.439 1.459 1.258 156 1140 1.485 .963 140 9780 4690 462 476 971 985 100 641 45 596 1.004 682 637 .996 1.02 .005 .028
17 312 483 81 66 231 417 255 385 84 68 174 319 0 0 417 683 24 18 100 100 98 100 648 493 .554 1.805 1.833 1.866 1.892 1.329 156 1272 1.508 .964 150 10180 4690 461 476 1010 1025 100 330 45 285 1.234 263 218 .81 1.253 .304 .326
18 4148 4678 84 71 4064 4607 4544 5136 88 73 4460 5065 0 0 1338 1451 44 20 100 100 100 100 8671 9525 .882 1.134 1.136 1.163 1.132 1.163 120 940 1.124 .988 130 10540 4710 464 477 1047 1060 100 3198 49 3150 .775 3511 3463 1.29 .776 -.368 -.365
19 1070 1225 82 69 988 1156 1054 1189 86 72 972 1120 0 0 189 259 25 19 100 100 100 100 2144 2092 .855 1.17 1.152 1.163 1.15 1.136 156 1272 1.197 .968 150 10930 4690 461 476 1085 1100 100 838 47 790 .8 813 766 1.25 .788 -.322 -.344
20 12420 14694 82 68 12338 14626 14520 16612 85 72 14438 16544 0 0 5091 5339 27 39 100 100 100 100 26964 30982 .844 1.185 1.146 1.255 1.153 1.332 156 1140 1.162 .987 140 11300 4680 461 475 1123 1137 100 10046 46 10000 .81 11357 11311 1.234 .783 -.303 -.352

Total number of rows: 24288

Table truncated, full table size 5448 Kbytes.




Supplementary file Size Download File type/resource
GSM498980.gpr.gz 2.1 Mb (ftp)(http) GPR
Processed data included within Sample table
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