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Sample GSM498977 Query DataSets for GSM498977
Status Public on Jan 21, 2010
Title AD3_REP1_ROOT
Sample type RNA
 
Channel 1
Source name AD3 salt root
Organism Gossypium tomentosum
Characteristics treatment: salt
name: wt936
genome: ad3
polyploid level: 4x
tissue type: root
Treatment protocol BYU growth chamber
Extracted molecule total RNA
Extraction protocol Date performed = 10/17/07; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD3 salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"
Label Cy3
Label protocol Approx RNA yield = 15 ug; Type of in-vitro transcription = Epicentre; Date performed = Mar-08; 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 salt root; Date performed = 3/15/2008; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura
 
Channel 2
Source name AD3 no-salt root
Organism Gossypium tomentosum
Characteristics treatment: no-salt
name: wt936
genome: ad3
tissue type: root
polyploid level: 4x
Treatment protocol BYU growth chamber
Extracted molecule total RNA
Extraction protocol Date performed = 10/17/07; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD3 no-salt root; 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 = 10 ug; Date performed = Mar-08; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 3/15/2008; Tube label = AD3 no-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 = 3/20/2008
Scanner Make = Agilent; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 3/20/2008
Description Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58080.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 1400 1780 75 54 1325 1726 1580 2022 77 55 1505 1968 0 0 469 616 19 11 100 100 100 100 3051 3473 .768 1.303 1.308 1.261 1.318 1.36 120 940 1.303 .975 130 3960 4110 404 417 389 402 100 1501 46 1456 1.099 1706 1660 .91 1.103 .136 .141
2 175 133 74 53 101 80 151 115 75 54 77 62 0 0 92 59 15 9 89 99 79 95 181 139 1.263 .792 .805 .94 .842 1.839 120 940 .681 .833 130 4360 4120 405 418 429 442 0 112 45 67 .668 97 52 1.497 .679 -.582 -.558
3 7527 7727 76 54 7451 7673 7832 7898 77 56 7756 7844 0 0 2120 1950 13 11 100 100 100 100 15124 15600 .971 1.03 1.011 1.041 1.019 1.151 120 940 1.02 .979 130 4750 4110 404 417 468 481 100 6518 46 6472 .869 6662 6616 1.151 .853 -.203 -.229
4 410 678 76 54 334 624 413 683 77 55 337 629 0 0 70 112 15 11 100 100 100 100 958 966 .535 1.868 1.866 1.88 1.898 1.189 120 940 1.863 .945 130 5110 4130 406 419 504 517 100 572 46 526 1.576 576 531 .635 1.574 .656 .655
5 373 276 75 54 298 222 383 277 76 55 308 223 0 0 89 51 14 10 100 100 100 100 520 531 1.342 .745 .724 .76 .734 1.274 80 656 .711 .886 110 5510 4110 405 416 545 556 100 233 46 187 .628 234 188 1.591 .611 -.67 -.711
6 746 965 76 56 670 909 100 433 79 57 24 377 0 0 846 856 111 15 44 100 43 100 1579 401 .737 1.357 15.708 3.568 1.309 4.849 460 3260 1.13 .957 240 5890 4130 401 425 577 601 100 814 47 767 1.144 365 318 .874 13.25 .195 3.728
7 784 727 76 53 708 674 799 752 77 54 723 699 0 0 227 187 14 11 100 100 100 100 1382 1422 1.05 .952 .967 .972 .957 1.235 120 820 .933 .958 120 6280 4110 405 417 622 634 100 613 45 569 .803 634 590 1.245 .816 -.317 -.294
8 4016 2776 76 53 3940 2723 4434 3168 76 54 4358 3115 0 0 1016 804 13 10 100 100 100 100 6663 7473 1.447 .691 .715 .678 .698 1.221 120 820 .697 .985 120 6650 4110 405 417 659 671 100 2342 45 2297 .583 2672 2628 1.715 .603 -.779 -.73
9 110 106 73 52 37 54 109 106 74 54 36 54 0 0 22 19 13 18 86 96 70 82 91 90 .685 1.459 1.5 1.723 1.667 2.336 80 560 1.237 .432 100 7030 4100 405 415 698 708 0 89 44 46 1.231 89 46 .812 1.265 .3 .339
10 4032 2747 77 52 3955 2695 4046 2796 79 56 3969 2744 0 0 398 257 31 30 100 100 100 100 6650 6713 1.468 .681 .691 .682 .678 1.072 80 656 .687 .975 110 7430 4120 406 417 737 748 100 2317 44 2273 .575 2358 2315 1.74 .583 -.799 -.778
11 415 434 75 53 340 381 416 413 76 54 341 360 0 0 169 196 13 9 99 100 97 99 721 701 .892 1.121 1.056 1.151 1.123 1.322 120 820 1.123 .955 120 7810 4130 407 419 775 787 100 366 45 321 .945 348 304 1.058 .891 -.081 -.167
12 33024 32059 79 55 32945 32004 36173 34382 82 57 36094 34327 0 0 8104 7726 24 15 100 100 100 100 64949 70421 1.029 .971 .951 .971 .975 1.24 120 940 .965 .969 130 8180 4100 403 416 811 824 100 27042 46 26996 .819 29001 28955 1.22 .802 -.287 -.318
13 297 253 76 53 221 200 293 252 77 54 217 199 0 0 89 49 15 10 100 100 100 100 421 416 1.105 .905 .917 .928 .949 1.373 120 940 .36 .368 130 8560 4120 405 418 849 862 0 213 45 169 .763 213 168 1.31 .774 -.39 -.37
14 2627 2782 78 54 2549 2728 2679 2844 79 55 2601 2790 0 0 464 454 17 9 100 100 100 100 5277 5391 .934 1.07 1.073 1.074 1.063 1.112 120 940 1.067 .979 130 8960 4120 405 418 889 902 100 2347 46 2301 .903 2399 2353 1.108 .905 -.148 -.144
15 530 703 76 54 454 649 550 739 79 56 474 685 0 0 167 238 60 23 98 99 94 98 1103 1159 .7 1.43 1.445 1.417 1.447 1.508 208 1512 1.435 .908 160 9320 4110 403 419 924 940 100 593 46 547 1.206 623 578 .829 1.219 .27 .286
16 3024 1929 77 54 2947 1875 2957 1909 78 55 2880 1855 0 0 631 372 17 11 100 100 100 100 4822 4735 1.572 .636 .644 .639 .634 1.121 156 1272 .632 .983 150 9710 4110 403 418 963 978 100 1627 46 1582 .537 1610 1565 1.863 .543 -.898 -.88
17 547 411 76 54 471 357 440 342 78 55 364 288 0 0 391 262 25 10 98 99 96 98 828 652 1.319 .758 .791 .8 .802 1.668 208 1660 .67 .895 170 10090 4120 403 420 1000 1017 100 347 46 301 .639 288 243 1.564 .667 -.645 -.583
18 3095 4372 77 54 3018 4318 3229 4519 78 55 3152 4465 0 0 558 755 15 10 100 100 100 100 7336 7617 .699 1.431 1.417 1.437 1.436 1.184 120 940 1.431 .971 130 10470 4090 402 415 1040 1053 100 3688 46 3642 1.207 3812 3766 .829 1.195 .271 .257
19 971 790 75 54 896 736 970 816 77 55 895 762 0 0 312 194 16 11 99 100 99 100 1632 1657 1.217 .821 .851 .85 .829 1.319 208 1512 .791 .929 160 10860 4110 403 419 1078 1094 100 666 46 621 .693 688 643 1.443 .718 -.529 -.478
20 29722 12689 76 54 29646 12635 33417 14204 79 55 33341 14150 0 0 10429 4517 23 11 100 100 100 100 42281 47491 2.346 .426 .424 .43 .434 1.431 156 1140 .421 .966 140 11220 4090 402 416 1115 1129 100 10703 46 10658 .359 11981 11936 2.782 .358 -1.476 -1.482

Total number of rows: 24288

Table truncated, full table size 5337 Kbytes.




Supplementary file Size Download File type/resource
GSM498977.gpr.gz 2.0 Mb (ftp)(http) GPR
Processed data included within Sample table
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