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Sample GSM498988 Query DataSets for GSM498988
Status Public on Jan 21, 2010
Title AD4_REP1_ROOT
Sample type RNA
 
Channel 1
Source name AD4 salt root
Organism Gossypium mustelinum
Characteristics treatment: salt
name: 15-c
genome: ad4
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 = AD4 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 = 14 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 = AD4 salt root; Date performed = 3/15/2008; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura
 
Channel 2
Source name AD4 no-salt root
Organism Gossypium mustelinum
Characteristics treatment: no-salt
name: 15-c
genome: ad4
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 = AD4 no-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 = 20 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 = AD4 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//58086.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 4293 5341 84 97 4209 5244 4598 5668 89 101 4514 5571 0 0 1364 1490 88 41 100 100 100 100 9453 10085 .803 1.246 1.234 1.29 1.235 1.27 120 940 1.23 .975 130 3850 3990 392 405 378 391 100 3553 65 3488 .829 3770 3706 1.207 .821 -.271 -.285
2 188 221 81 83 107 138 177 213 84 88 96 130 0 0 71 85 25 31 88 91 73 83 245 226 .775 1.29 1.354 1.347 1.344 1.794 80 560 1.258 .773 100 4220 3990 394 404 417 427 0 147 55 92 .858 142 86 1.166 .901 -.221 -.151
3 14397 16791 82 79 14315 16712 15393 17364 85 81 15311 17285 0 0 5278 5133 22 22 100 100 100 100 31027 32596 .857 1.167 1.129 1.216 1.157 1.219 120 940 1.138 .976 130 4620 3990 392 405 455 468 100 11169 53 11117 .777 11550 11498 1.288 .751 -.365 -.413
4 1508 1704 81 78 1427 1626 1565 1778 82 80 1484 1700 0 0 329 396 15 16 100 100 100 100 3053 3184 .878 1.139 1.146 1.121 1.145 1.233 120 940 1.147 .972 130 4990 4010 394 407 492 505 100 1133 52 1082 .758 1183 1131 1.319 .762 -.4 -.392
5 256 305 81 74 175 231 258 319 83 104 177 245 0 0 73 74 29 372 96 1 93 0 406 422 .758 1.32 1.384 1.396 1.329 1.424 120 940 1.272 .881 130 5380 4000 393 406 531 544 100 203 49 154 .878 212 163 1.139 .921 -.188 -.119
6 1356 1265 80 74 1276 1191 454 542 82 86 374 468 0 0 1398 1067 21 210 60 82 55 52 2467 842 1.071 .933 1.251 2.376 .905 4.984 392 2972 .827 .975 230 5770 4020 390 413 565 588 100 841 49 792 .621 361 311 1.611 .832 -.688 -.265
7 1169 1399 80 70 1089 1329 1216 1450 81 71 1136 1380 0 0 316 366 15 12 100 100 100 100 2418 2516 .819 1.22 1.215 1.233 1.218 1.173 120 940 1.216 .979 130 6160 4000 393 406 609 622 100 931 47 884 .812 965 918 1.232 .808 -.301 -.307
8 4871 6458 80 69 4791 6389 5236 6891 87 72 5156 6822 0 0 1173 1365 89 31 100 100 100 100 11180 11978 .75 1.334 1.323 1.346 1.331 1.14 120 940 1.323 .986 130 6540 3990 392 405 647 660 100 4296 46 4250 .887 4584 4538 1.127 .88 -.173 -.184
9 108 132 77 65 31 67 107 130 79 67 30 65 0 0 22 25 17 13 70 97 41 96 98 95 .463 2.161 2.167 2.669 2.306 2.598 80 656 1.716 .417 110 6910 4000 394 405 685 696 0 88 43 45 1.438 86 43 .696 1.441 .524 .527
10 5261 4600 80 67 5181 4533 5678 4966 82 69 5598 4899 0 0 1367 1132 19 16 100 100 100 100 9714 10497 1.143 .875 .875 .877 .867 1.152 120 940 .87 .985 130 7300 3990 392 405 723 736 100 3060 45 3015 .582 3303 3259 1.718 .582 -.781 -.781
11 376 528 80 68 296 460 355 479 80 84 275 411 0 0 146 221 15 207 100 90 100 48 756 686 .643 1.554 1.495 1.583 1.545 1.212 120 940 3.062 .436 130 7690 3990 392 405 762 775 100 351 45 306 1.034 319 273 .967 .994 .048 -.008
12 28552 21574 82 68 28470 21506 30493 22764 87 71 30411 22696 0 0 5775 4475 40 31 100 100 100 100 49976 53107 1.324 .755 .746 .753 .755 1.07 120 940 .756 .996 130 8060 3990 392 405 799 812 100 14351 45 14306 .502 15142 15097 1.99 .496 -.993 -1.01
13 205 233 78 65 127 168 209 235 81 66 131 170 0 0 62 69 30 15 92 100 82 98 295 301 .756 1.323 1.298 1.444 1.354 1.607 156 1140 1.288 .836 140 8440 4000 393 407 837 851 0 155 43 112 .88 156 113 1.136 .863 -.185 -.212
14 7235 6410 81 66 7154 6344 7379 6513 83 67 7298 6447 0 0 1245 978 19 15 100 100 100 100 13498 13745 1.128 .887 .883 .891 .874 1.106 120 940 .881 .989 130 8840 3980 391 404 877 890 100 4264 44 4220 .59 4332 4288 1.695 .588 -.762 -.767
15 1704 1707 81 66 1623 1641 1694 1721 89 72 1613 1655 0 0 336 313 155 80 100 100 100 100 3264 3268 .989 1.011 1.026 1.016 1.02 1.108 156 1272 1.012 .978 150 9210 3990 391 406 913 928 100 1135 44 1092 .673 1145 1101 1.487 .683 -.572 -.551
16 1301 2045 81 66 1220 1979 1303 2038 82 68 1222 1972 0 0 251 372 19 29 100 100 100 100 3199 3194 .616 1.622 1.614 1.632 1.617 1.142 156 1272 1.619 .973 150 9590 4000 392 407 951 966 100 1360 44 1316 1.079 1356 1312 .927 1.073 .11 .102
17 587 546 79 67 508 479 583 551 81 70 504 484 0 0 105 91 23 65 100 100 100 100 987 988 1.061 .943 .96 .946 .96 1.195 156 1272 .937 .943 150 9990 3990 391 406 991 1006 100 363 45 319 .627 367 322 1.594 .639 -.673 -.647
18 7868 8300 82 65 7786 8235 7977 8462 83 66 7895 8397 0 0 1949 2044 16 12 100 100 100 100 16021 16292 .945 1.058 1.064 1.058 1.079 1.136 120 940 1.057 .977 130 10370 3980 391 404 1030 1043 100 5521 43 5478 .704 5629 5586 1.421 .707 -.507 -.499
19 1702 1822 81 67 1621 1755 1638 1799 83 69 1557 1732 0 0 534 515 17 14 100 100 100 100 3376 3289 .924 1.083 1.112 1.097 1.076 1.187 208 1512 1.068 .975 160 10750 4000 392 408 1067 1083 100 1212 45 1167 .72 1197 1152 1.389 .74 -.474 -.434
20 21445 16472 81 68 21364 16404 23905 18005 83 69 23824 17937 0 0 7446 4961 17 12 100 100 100 100 37768 41761 1.302 .768 .753 .805 .755 1.287 156 1140 .753 .986 140 11130 3980 391 405 1106 1120 100 10957 45 10912 .511 11977 11932 1.958 .501 -.969 -.998

Total number of rows: 24288

Table truncated, full table size 5457 Kbytes.




Supplementary file Size Download File type/resource
GSM498988.gpr.gz 2.1 Mb (ftp)(http) GPR
Processed data included within Sample table
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