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Sample GSM498982 Query DataSets for GSM498982
Status Public on Jan 21, 2010
Title AD1_REP3_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 = Jun-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 2 plants"
Label Cy3
Label protocol Approx RNA yield = 16 ug; Type of in-vitro transcription = Epicentre; Date performed = Jul-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 = 7/23/2007; 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 = Jun-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 2 plants"; Name = Rozaura; Extracted molecule = RNA
Label Cy5
Label protocol Approx RNA yield = 15.5 ug; Date performed = Jul-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 = 7/23/2007; 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 = 7/26/2007
Scanner Make = Agilent; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 7/26/2007
Description Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58067.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 1439 5754 76 83 1363 5671 1545 6390 76 85 1469 6307 0 0 406 1799 14 15 100 100 100 100 7034 7776 .24 4.161 4.293 4.102 4.224 1.172 120 940 4.214 .984 130 3990 4390 432 445 392 405 100 1628 23 1604 1.177 1807 1784 .85 1.214 .235 .28
2 923 4193 76 84 847 4109 703 3015 82 102 627 2931 0 0 596 2879 30 108 99 100 98 100 4956 3558 .206 4.851 4.675 5.067 4.587 1.566 120 940 4.966 .956 130 4390 4400 433 446 432 445 100 1186 24 1162 1.372 853 829 .729 1.322 .457 .403
3 3298 12188 75 82 3223 12106 3273 12437 75 82 3198 12355 0 0 857 2612 13 14 100 100 100 100 15329 15553 .266 3.756 3.863 3.787 3.878 1.22 120 940 3.794 .941 130 4760 4400 433 446 469 482 100 3448 23 3424 1.062 3518 3495 .941 1.093 .087 .128
4 346 1285 75 83 271 1202 343 1317 76 85 268 1234 0 0 72 297 13 17 100 100 99 100 1473 1502 .225 4.435 4.604 4.509 4.449 1.444 120 940 4.512 .902 130 5140 4410 434 447 507 520 100 363 23 340 1.255 373 349 .797 1.302 .327 .381
5 774 2392 75 81 699 2311 821 2538 76 83 746 2457 0 0 201 661 16 19 100 100 100 100 3010 3203 .302 3.306 3.294 3.306 3.32 1.189 120 820 3.347 .976 120 5510 4400 434 446 545 557 100 677 23 654 .935 718 695 1.069 .932 -.097 -.102
6 1312 1969 76 84 1236 1885 99 344 77 87 23 260 0 0 1651 2349 14 19 54 100 48 100 3121 283 .656 1.525 11.304 4.167 1.73 4.145 460 3270 1.456 .98 240 5890 4420 430 454 577 601 100 557 24 533 .431 97 74 2.318 3.198 -1.213 1.677
7 870 2632 78 85 792 2547 953 2940 78 85 875 2855 0 0 269 856 14 15 100 100 100 100 3339 3730 .311 3.216 3.263 3.239 3.269 1.242 120 820 3.245 .969 120 6290 4400 434 446 623 635 100 744 24 720 .91 832 808 1.099 .923 -.137 -.116
8 212 680 77 83 135 597 217 736 79 85 140 653 0 0 52 200 19 18 97 100 95 100 732 793 .226 4.422 4.664 4.615 4.742 1.554 120 820 4.647 .821 120 6680 4430 437 449 662 674 100 192 23 169 1.251 208 185 .799 1.319 .323 .4
9 135 233 77 81 58 152 126 214 82 86 49 133 0 0 40 75 42 34 57 100 18 92 210 182 .382 2.621 2.714 3.062 2.797 1.906 80 656 1.49 .485 110 7070 4400 434 445 701 712 0 66 23 43 .741 61 38 1.349 .768 -.432 -.381
10 437 1280 76 84 361 1196 440 1426 78 86 364 1342 0 0 154 431 15 16 100 100 99 100 1557 1706 .302 3.313 3.687 3.352 3.411 1.309 120 820 3.332 .924 120 7450 4390 433 445 739 751 100 362 24 338 .937 403 380 1.067 1.043 -.094 .061
11 289 1165 79 86 210 1079 283 1287 80 87 204 1201 0 0 93 470 15 16 98 100 97 100 1289 1405 .195 5.138 5.887 4.814 5.618 1.626 120 820 5.715 .787 120 7830 4390 433 445 777 789 100 330 24 305 1.453 364 340 .688 1.665 .539 .736
12 1329 6607 86 93 1243 6514 1347 7106 88 95 1261 7013 0 0 291 1514 20 18 100 100 100 100 7757 8274 .191 5.241 5.561 5.305 5.475 1.396 120 820 5.427 .925 120 8200 4400 434 446 814 826 100 1869 26 1843 1.482 2010 1984 .675 1.573 .568 .654
13 487 983 76 81 411 902 487 1022 83 85 411 941 0 0 100 259 96 36 100 100 100 100 1313 1352 .456 2.195 2.29 2.156 2.218 1.308 120 940 2.067 .69 130 8590 4410 434 447 852 865 100 278 23 255 .621 289 266 1.611 .648 -.688 -.627
14 3058 11753 74 73 2984 11680 3269 12401 76 75 3195 12328 0 0 861 2979 14 16 100 100 100 100 14664 15523 .255 3.914 3.859 4.029 3.912 1.26 120 820 3.907 .977 120 8970 4400 434 446 891 903 100 3324 21 3304 1.107 3508 3487 .903 1.091 .147 .126
15 438 1990 73 74 365 1916 451 2020 74 76 378 1946 0 0 102 457 13 15 100 100 100 100 2281 2324 .191 5.249 5.148 5.396 5.15 1.284 156 1140 5.255 .949 140 9360 4420 435 449 929 943 100 563 21 542 1.485 571 550 .673 1.456 .57 .542
16 2931 62995 73 74 2858 62921 3045 65249 73 75 2972 65175 0 0 771 8100 13 28 100 100 100 100 65779 68147 .045 22.016 21.93 23.035 21.889 1.34 156 1272 22.41 .925 150 9730 4410 433 448 965 980 100 17819 21 17798 6.227 18456 18435 .161 6.203 2.639 2.633
17 155 478 72 74 83 404 155 486 73 75 83 412 0 0 40 93 13 14 97 100 94 100 487 495 .205 4.867 4.964 5.234 4.923 1.624 156 1140 4.764 .619 140 10120 4420 435 449 1005 1019 100 135 21 114 1.377 137 117 .726 1.404 .461 .49
18 1941 8228 73 74 1868 8154 2138 9335 74 75 2065 9261 0 0 566 2776 13 14 100 100 100 100 10022 11326 .229 4.365 4.485 4.285 4.468 1.274 120 820 4.493 .971 120 10500 4400 434 446 1044 1056 100 2327 21 2306 1.235 2641 2620 .81 1.269 .304 .343
19 602 2174 73 74 529 2100 593 2058 75 76 520 1984 0 0 135 525 16 17 100 100 100 100 2629 2504 .252 3.97 3.815 3.968 3.996 1.191 156 1272 4.076 .95 150 10880 4430 435 450 1080 1095 100 615 21 594 1.123 582 561 .891 1.079 .167 .11
20 4372 16768 73 75 4299 16693 4715 17472 74 76 4642 17397 0 0 1085 3264 14 17 100 100 100 100 20992 22039 .258 3.883 3.748 4.027 3.813 1.225 120 940 3.828 .983 130 11270 4440 437 450 1120 1133 100 4743 21 4722 1.098 4942 4921 .91 1.06 .135 .084

Total number of rows: 24288

Table truncated, full table size 5437 Kbytes.




Supplementary file Size Download File type/resource
GSM498982.gpr.gz 2.1 Mb (ftp)(http) GPR
Processed data included within Sample table
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