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Sample GSM498979 Query DataSets for GSM498979
Status Public on Jan 21, 2010
Title AD3_REP2_LEAF
Sample type RNA
 
Channel 1
Source name AD3 no-salt leaf
Organism Gossypium tomentosum
Characteristics treatment: no-salt
name: wt936
genome: ad3
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 = AD3 no-salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 3 plants"
Label Cy3
Label protocol Approx RNA yield = 50 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 = AD3 no-salt leaf; Date performed = 9/5/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura
 
Channel 2
Source name AD3 salt leaf
Organism Gossypium tomentosum
Characteristics treatment: salt
name: wt936
genome: ad3
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 = AD3 salt leaf; 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 = 42.5 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 = AD3 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//58081.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 2322 3046 129 121 2193 2925 2207 3171 132 120 2078 3050 0 0 856 971 23 20 100 100 100 100 5118 5128 .75 1.334 1.468 1.358 1.333 1.233 120 940 1.318 .953 130 3500 4950 488 501 343 356 100 1751 70 1681 .767 1823 1753 1.304 .844 -.383 -.245
2 2732 3599 131 121 2601 3478 2254 2919 137 126 2123 2798 0 0 1366 1895 44 43 100 100 100 100 6079 4921 .748 1.337 1.318 1.321 1.305 1.164 120 940 1.36 .978 130 3900 4950 488 501 383 396 100 2069 70 1999 .769 1678 1608 1.301 .757 -.38 -.401
3 5716 7330 130 115 5586 7215 5901 7478 131 115 5771 7363 0 0 1346 1285 23 21 100 100 100 100 12801 13134 .774 1.292 1.276 1.318 1.234 1.255 120 940 1.296 .933 130 4280 4950 488 501 421 434 100 4213 66 4147 .742 4298 4232 1.347 .733 -.43 -.448
4 1241 1455 129 117 1112 1338 1230 1450 139 118 1101 1333 0 0 273 247 252 27 100 100 99 100 2450 2434 .831 1.203 1.211 1.222 1.199 1.212 120 940 1.193 .935 130 4680 4960 489 502 461 474 100 836 67 769 .692 833 766 1.446 .696 -.532 -.523
5 1440 1638 130 116 1310 1522 1481 1686 132 115 1351 1570 0 0 358 318 23 19 100 100 100 100 2832 2921 .861 1.162 1.162 1.172 1.178 1.22 120 940 1.149 .947 130 5050 4960 489 502 498 511 100 941 67 875 .668 969 902 1.498 .668 -.583 -.582
6 5275 5685 126 126 5149 5559 5925 6202 128 138 5799 6076 0 0 2647 2478 22 42 100 100 100 100 10708 11875 .926 1.08 1.048 1.197 1.04 1.635 208 1660 1.035 .956 170 5440 4970 488 505 535 552 100 3267 72 3195 .621 3565 3492 1.612 .602 -.688 -.732
7 3414 5159 125 113 3289 5046 3510 5072 128 115 3385 4959 0 0 1028 1858 25 21 100 100 100 100 8335 8344 .652 1.534 1.465 1.512 1.539 1.229 120 820 1.578 .971 120 5830 4950 489 501 577 589 100 2965 65 2900 .882 2915 2850 1.134 .842 -.181 -.248
8 734 773 126 111 608 662 751 822 128 111 625 711 0 0 205 203 22 20 100 100 99 100 1270 1336 .918 1.089 1.138 1.108 1.116 1.351 120 820 1.09 .91 120 6200 4940 488 500 614 626 100 444 64 380 .626 472 409 1.598 .654 -.676 -.613
9 291 254 126 111 165 143 281 251 127 112 155 140 0 0 79 45 25 23 100 100 98 98 308 295 1.154 .867 .903 .918 .942 1.535 80 560 .806 .763 100 6580 4950 490 500 653 663 0 146 64 82 .498 144 80 2.008 .519 -1.005 -.946
10 467 347 127 110 340 237 456 343 129 111 329 233 0 0 144 78 23 18 100 100 100 99 577 562 1.435 .697 .708 .719 .725 1.465 120 820 .666 .858 120 6950 4960 490 502 689 701 100 199 63 136 .401 197 134 2.496 .407 -1.32 -1.297
11 966 1318 126 110 840 1208 1028 1396 131 113 902 1286 0 0 333 478 54 33 99 100 98 99 2048 2188 .695 1.438 1.426 1.449 1.489 1.478 120 820 1.449 .949 120 7350 4930 487 499 729 741 100 758 63 694 .827 802 739 1.21 .819 -.275 -.287
12 4997 3114 125 110 4872 3004 5341 3314 127 111 5216 3204 0 0 1423 784 23 19 100 100 100 100 7876 8420 1.622 .617 .614 .64 .627 1.48 120 940 .607 .959 130 7730 4960 489 502 766 779 100 1790 63 1727 .354 1905 1842 2.822 .353 -1.497 -1.502
13 697 756 125 110 572 646 686 746 126 111 561 636 0 0 163 186 23 22 100 100 100 100 1218 1197 .885 1.129 1.134 1.134 1.177 1.306 120 940 1.135 .921 130 8110 4950 488 501 804 817 100 435 63 371 .649 429 366 1.541 .652 -.623 -.618
14 4119 4607 122 106 3997 4501 4050 4559 125 107 3928 4453 0 0 993 866 23 19 100 100 100 100 8498 8381 .888 1.126 1.134 1.149 1.097 1.193 120 820 1.107 .973 120 8510 4940 488 500 845 857 100 2648 61 2587 .647 2620 2559 1.545 .652 -.628 -.618
15 855 872 123 107 732 765 863 870 124 107 740 763 0 0 249 208 22 19 99 100 99 100 1497 1503 .957 1.045 1.031 1.091 1.079 1.381 156 1140 1.028 .943 140 8890 4950 488 502 882 896 100 501 61 440 .601 500 439 1.665 .593 -.735 -.755
16 675 728 125 108 550 620 678 725 127 109 553 617 0 0 249 217 23 19 99 100 96 100 1170 1170 .887 1.127 1.116 1.192 1.187 1.414 156 1140 1.063 .898 140 9270 4950 488 502 920 934 100 418 62 356 .648 417 355 1.543 .641 -.626 -.641
17 643 627 125 109 518 518 641 652 127 109 516 543 0 0 261 182 22 18 98 100 98 98 1036 1059 1 1 1.052 1.067 1.059 1.553 156 1140 .933 .871 140 9670 4950 488 502 960 974 100 360 63 298 .575 375 312 1.74 .605 -.799 -.725
18 4249 3766 127 109 4122 3657 4123 3828 128 110 3996 3719 0 0 1060 1020 23 18 100 100 100 100 7779 7715 1.127 .887 .931 .868 .898 1.314 120 820 .893 .96 120 10030 4930 487 499 997 1009 100 2165 63 2102 .51 2200 2138 1.961 .535 -.972 -.903
19 953 1026 125 107 828 919 946 1027 126 108 821 920 0 0 233 243 22 19 100 100 100 100 1747 1741 .901 1.11 1.121 1.112 1.117 1.221 156 1272 1.102 .96 150 10410 4940 486 501 1033 1048 100 590 61 528 .638 590 529 1.568 .644 -.649 -.635
20 6249 6923 124 108 6125 6815 6469 7096 125 108 6345 6988 0 0 1419 1415 22 20 100 100 100 100 12940 13333 .899 1.113 1.101 1.122 1.132 1.157 120 940 1.099 .97 130 10800 4930 486 499 1073 1086 100 3979 62 3917 .64 4078 4016 1.564 .633 -.645 -.66

Total number of rows: 24288

Table truncated, full table size 5535 Kbytes.




Supplementary file Size Download File type/resource
GSM498979.gpr.gz 2.1 Mb (ftp)(http) GPR
Processed data included within Sample table
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