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Sample GSM498986 Query DataSets for GSM498986
Status Public on Jan 21, 2010
Title AD1_REP4_LEAF
Sample type RNA
 
Channel 1
Source name AD1 salt leaf
Organism Gossypium hirsutum
Characteristics treatment: salt
name: tm1
genome: ad1
polyploid level: 4x
tissue type: leaf
Treatment protocol BYU growth chamber
Extracted molecule total RNA
Extraction protocol Date performed = Jul-07; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD1 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 = 15 ug; Type of in-vitro transcription = Epicentre; Date performed = Aug-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 = AD1 salt leaf; Date performed = 8/17/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura
 
Channel 2
Source name AD1 no-salt leaf
Organism Gossypium hirsutum
Characteristics treatment: no-salt
name: tm1
genome: ad1
tissue type: leaf
polyploid level: 4x
Treatment protocol BYU growth chamber
Extracted molecule total RNA
Extraction protocol Date performed = Jul-07; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD1 no-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 = 12 ug; Date performed = Aug-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 = 8/17/2007; Tube label = AD1 no-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 = 8/28/2007
Scanner Make = Agilent; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 8/28/2007
Description Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58069.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 1831 3481 172 87 1659 3394 1864 3608 175 88 1692 3521 0 0 537 1172 28 19 100 100 100 100 5053 5213 .489 2.046 2.081 2.025 2.032 1.232 120 940 2.074 .966 130 3840 5160 509 522 377 390 100 1393 35 1358 .819 1444 1409 1.221 .833 -.289 -.264
2 1198 2244 175 87 1023 2157 1131 2020 178 92 956 1933 0 0 463 1066 35 42 100 100 100 100 3180 2889 .474 2.109 2.022 2.106 2.113 1.21 120 820 2.137 .96 120 4230 5170 511 523 417 429 100 898 35 863 .844 808 774 1.185 .809 -.245 -.306
3 5327 6832 176 88 5151 6744 5158 6970 177 91 4982 6882 0 0 1490 1591 30 22 100 100 100 100 11895 11864 .764 1.309 1.381 1.328 1.302 1.178 120 940 1.319 .955 130 4620 5160 509 522 455 468 100 2734 35 2699 .524 2789 2754 1.909 .553 -.933 -.855
4 533 897 173 87 360 810 529 892 176 88 356 805 0 0 90 164 30 16 100 100 100 100 1170 1161 .444 2.25 2.261 2.277 2.275 1.218 120 940 2.178 .924 130 5010 5180 511 524 494 507 100 359 35 324 .9 357 322 1.111 .905 -.151 -.144
5 1337 2382 189 90 1148 2292 1424 2551 191 91 1235 2461 0 0 298 520 32 18 100 100 100 100 3440 3696 .501 1.997 1.993 2.027 1.978 1.169 120 820 1.981 .981 120 5390 5170 511 523 533 545 100 953 36 917 .799 1021 985 1.252 .797 -.324 -.327
6 4495 5040 190 114 4305 4926 4632 5164 192 135 4442 5050 0 0 829 1021 43 65 100 100 100 100 9231 9492 .874 1.144 1.137 1.136 1.144 1.151 156 1272 1.125 .979 150 5770 5180 510 525 569 584 100 2017 46 1971 .458 2067 2021 2.184 .455 -1.127 -1.136
7 811 2488 199 95 612 2393 897 2870 200 99 698 2775 0 0 260 1077 31 23 97 100 94 100 3005 3473 .256 3.91 3.976 4.055 3.989 1.612 156 1140 3.982 .95 140 6160 5160 509 523 609 623 100 996 38 958 1.565 1149 1110 .639 1.591 .646 .67
8 279 629 203 95 76 534 277 657 204 96 74 562 0 0 43 117 31 23 82 100 60 100 610 636 .142 7.026 7.595 8.122 7.338 1.997 80 656 6.315 .571 110 6520 5160 510 521 646 657 100 252 38 214 2.812 263 225 .356 3.039 1.491 1.604
9 112 104 193 91 -81 13 104 101 194 91 -89 10 0 0 31 27 33 16 0 42 0 30 -68 -79 null null null .222 .2 3.247 120 940 6.178 .088 130 6930 5160 509 522 686 699 -50 42 36 5 null 40 4 null null null null
10 451 903 190 88 261 815 465 954 190 89 275 866 0 0 90 217 29 15 98 100 97 100 1076 1141 .32 3.123 3.149 3.289 3.07 1.466 120 820 3.028 .876 120 7290 5150 509 521 723 735 100 361 35 326 1.25 382 347 .8 1.26 .321 .334
11 334 800 199 91 135 709 343 884 199 92 144 793 0 0 77 291 31 18 87 100 80 100 844 937 .19 5.252 5.507 5.742 5.308 1.788 120 820 4.796 .794 120 7690 5150 509 521 763 775 100 320 36 284 2.102 354 317 .476 2.204 1.072 1.14
12 1483 4786 204 96 1279 4690 1498 4782 211 103 1294 4686 0 0 239 666 98 69 100 100 100 100 5969 5980 .273 3.667 3.621 3.713 3.668 1.221 120 940 3.683 .951 130 8070 5160 509 522 800 813 100 1915 38 1877 1.467 1914 1875 .681 1.449 .553 .535
13 261 550 202 98 59 452 253 554 203 99 51 456 0 0 45 125 33 19 66 100 40 100 511 507 .131 7.661 8.941 9.646 7.947 2.459 120 820 6.089 .461 120 8470 5160 510 522 841 853 100 220 39 181 3.066 222 182 .326 3.578 1.616 1.839
14 1639 4580 203 100 1436 4480 1664 4601 206 102 1461 4501 0 0 288 868 32 20 100 100 100 100 5916 5962 .321 3.12 3.081 3.125 3.196 1.17 120 820 3.172 .952 120 8840 5150 509 521 878 890 100 1833 40 1793 1.248 1841 1801 .801 1.233 .32 .302
15 589 1104 204 108 385 996 564 1105 206 110 360 997 0 0 123 254 31 22 100 100 100 100 1381 1357 .387 2.587 2.769 2.616 2.733 1.437 156 1140 2.698 .821 140 9230 5170 510 524 916 930 100 442 43 399 1.035 442 399 .966 1.108 .05 .148
16 2297 4695 205 105 2092 4590 2223 4506 207 106 2018 4401 0 0 595 1146 32 21 100 100 100 100 6682 6419 .456 2.194 2.181 2.209 2.334 1.23 156 1272 2.202 .939 150 9600 5160 508 523 952 967 100 1879 42 1837 .878 1803 1761 1.139 .873 -.188 -.196
17 242 335 211 106 31 229 226 321 212 107 15 215 0 0 84 89 33 19 35 100 15 100 260 230 .135 7.387 14.333 6.468 5.371 2.786 120 940 3.579 .221 130 10000 5170 510 523 993 1006 100 134 42 92 2.956 128 86 .338 5.736 1.564 2.52
18 2111 4138 210 105 1901 4033 2237 4411 211 106 2027 4306 0 0 587 1321 30 19 100 100 100 100 5934 6333 .471 2.122 2.124 2.073 2.158 1.296 120 820 2.165 .943 120 10370 5140 508 520 1031 1043 100 1656 42 1614 .849 1765 1723 1.178 .85 -.236 -.234
19 1105 1498 211 102 894 1396 1039 1455 216 108 828 1353 0 0 292 366 94 82 100 100 100 100 2290 2181 .64 1.562 1.634 1.585 1.597 1.208 156 1272 1.493 .93 150 10750 5170 509 524 1067 1082 100 599 41 559 .625 582 541 1.6 .654 -.678 -.613
20 7353 11371 219 100 7134 11271 7486 12024 223 105 7267 11924 0 0 1808 2853 73 55 100 100 100 100 18405 19191 .633 1.58 1.641 1.571 1.619 1.273 120 940 1.591 .968 130 11130 5150 508 521 1106 1119 100 4550 40 4510 .632 4812 4772 1.582 .657 -.661 -.607

Total number of rows: 24288

Table truncated, full table size 5522 Kbytes.




Supplementary file Size Download File type/resource
GSM498986.gpr.gz 2.2 Mb (ftp)(http) GPR
Processed data included within Sample table
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