NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM498975 Query DataSets for GSM498975
Status Public on Jan 21, 2010
Title AD1_REP1_ROOT
Sample type RNA
 
Channel 1
Source name AD1 salt root
Organism Gossypium hirsutum
Characteristics treatment: salt
name: tm1
genome: ad1
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 = AD1 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 = 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 = AD1 salt root; Date performed = 3/15/2008; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura
 
Channel 2
Source name AD1 no-salt root
Organism Gossypium hirsutum
Characteristics treatment: no-salt
name: tm1
genome: ad1
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 = AD1 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 = 20ug; 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 = AD1 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//58063.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 4596 3452 82 63 4514 3389 4591 3458 83 63 4509 3395 0 0 1479 1128 15 12 100 100 100 100 7903 7904 1.332 .751 .753 .753 .758 1.159 120 940 .748 .981 130 3950 3860 379 392 388 401 100 2931 54 2878 .638 2937 2883 1.568 .639 -.649 -.645
2 124 135 78 59 46 76 113 126 79 61 35 67 0 0 50 57 15 12 67 92 52 80 122 102 .605 1.652 1.914 1.911 1.653 2.632 80 656 1.34 .666 110 4330 3840 378 389 427 438 0 115 50 65 1.403 107 57 .713 1.626 .489 .701
3 3304 2942 78 60 3226 2882 3243 2916 81 62 3165 2856 0 0 1373 1173 25 20 100 100 100 100 6108 6021 1.119 .893 .902 .897 .901 1.124 80 656 .885 .986 110 4710 3870 381 392 465 476 100 2498 51 2447 .759 2476 2425 1.318 .766 -.398 -.384
4 158 170 78 59 80 111 154 165 79 59 76 106 0 0 33 29 14 11 100 100 96 100 191 182 .721 1.388 1.395 1.462 1.389 1.542 80 656 1.301 .732 110 5080 3870 381 392 502 513 0 144 50 94 1.178 140 90 .849 1.184 .237 .244
5 348 340 80 60 268 280 347 360 82 61 267 300 0 0 115 109 30 11 99 100 94 100 548 567 .957 1.045 1.124 1.091 1.074 1.412 120 820 1.017 .919 120 5470 3870 381 393 541 553 100 289 51 238 .887 306 255 1.127 .954 -.173 -.068
6 1183 1169 82 64 1101 1105 100 379 83 67 18 315 0 0 4256 2344 18 19 49 100 45 100 2206 333 .996 1.004 17.5 2.995 1.28 4.605 460 3231 .57 .933 240 5860 3880 376 400 574 598 0 993 54 938 .852 322 268 1.173 14.861 -.231 3.893
7 1412 1551 80 60 1332 1491 1533 1660 81 61 1453 1600 0 0 443 444 15 11 100 100 100 100 2823 3053 .893 1.119 1.101 1.15 1.123 1.235 120 820 1.102 .979 120 6250 3870 381 393 619 631 100 1317 51 1266 .951 1410 1359 1.052 .935 -.073 -.097
8 3511 3341 82 62 3429 3279 3962 3655 83 63 3880 3593 0 0 1114 1002 16 12 100 100 100 100 6708 7473 1.046 .956 .926 .97 .954 1.149 120 820 .949 .99 120 6640 3860 380 392 658 670 100 2837 53 2785 .812 3104 3051 1.231 .786 -.3 -.347
9 119 152 81 61 38 91 112 116 83 63 31 55 0 0 67 286 16 13 69 91 45 85 129 86 .418 2.395 1.774 1.791 1.453 2.724 120 940 2.059 .948 130 7010 3860 379 392 694 707 0 129 52 77 2.034 99 47 .492 1.507 1.024 .591
10 4953 4208 82 62 4871 4146 5475 4560 84 63 5393 4498 0 0 1381 1131 17 11 100 100 100 100 9017 9891 1.175 .851 .834 .874 .861 1.204 120 940 .848 .989 130 7410 3860 379 392 734 747 100 3573 53 3521 .723 3872 3820 1.383 .708 -.468 -.498
11 719 903 81 61 638 842 703 873 83 65 622 812 0 0 330 464 21 49 99 97 98 97 1480 1434 .758 1.32 1.305 1.267 1.316 1.436 120 820 1.344 .975 120 7800 3860 380 392 774 786 100 767 52 715 1.121 741 690 .892 1.109 .164 .149
12 12983 16572 81 62 12902 16510 14039 17280 83 63 13958 17218 0 0 3240 3098 15 11 100 100 100 100 29412 31176 .781 1.28 1.234 1.316 1.236 1.227 120 940 1.261 .98 130 8170 3860 379 392 810 823 100 14073 53 14021 1.087 14674 14622 .92 1.048 .12 .067
13 305 342 80 61 225 281 302 350 83 63 222 289 0 0 60 67 27 20 100 100 100 100 506 511 .801 1.249 1.302 1.263 1.257 1.312 120 820 1.242 .882 120 8540 3880 382 394 848 860 100 290 52 239 1.061 297 245 .943 1.106 .085 .145
14 6037 5104 82 62 5955 5042 6246 5244 84 64 6164 5182 0 0 1174 943 25 21 100 100 100 100 10997 11346 1.181 .847 .841 .85 .847 1.132 120 940 .844 .979 130 8950 3870 380 393 888 901 100 4334 53 4282 .719 4453 4401 1.391 .714 -.476 -.486
15 2107 1625 80 62 2027 1563 2120 1649 81 62 2040 1587 0 0 368 262 15 11 100 100 100 100 3590 3627 1.297 .771 .778 .774 .765 1.111 156 1140 .768 .976 140 9340 3870 380 394 927 941 100 1380 53 1327 .655 1400 1348 1.527 .661 -.611 -.598
16 1781 1562 80 61 1701 1501 1835 1627 82 62 1755 1566 0 0 345 289 19 16 100 100 100 100 3202 3321 1.133 .882 .892 .885 .895 1.14 156 1140 .878 .981 140 9710 3870 380 394 964 978 100 1326 52 1275 .749 1382 1330 1.334 .758 -.416 -.4
17 385 348 80 61 305 287 385 350 83 64 305 289 0 0 64 54 34 28 100 100 100 100 592 594 1.063 .941 .948 .944 .933 1.218 156 1272 .911 .921 150 10090 3880 380 395 1001 1016 100 296 52 244 .799 297 245 1.251 .805 -.324 -.314
18 7798 5849 82 62 7716 5787 8288 6162 83 62 8206 6100 0 0 2046 1274 16 11 100 100 100 100 13503 14306 1.333 .75 .743 .766 .74 1.216 120 820 .736 .976 120 10470 3860 380 392 1041 1053 100 4967 53 4914 .637 5233 5180 1.57 .631 -.651 -.664
19 1703 1439 81 61 1622 1378 1641 1381 84 63 1560 1320 0 0 377 320 26 15 100 100 100 100 3000 2880 1.177 .85 .846 .85 .851 1.107 156 1272 .848 .979 150 10850 3870 379 394 1077 1092 100 1222 52 1170 .721 1173 1121 1.386 .719 -.471 -.477
20 22292 14783 86 63 22206 14720 23441 15451 88 65 23355 15388 0 0 3839 2331 21 19 100 100 100 100 36926 38743 1.509 .663 .659 .667 .662 1.149 120 940 .66 .986 130 11240 3860 379 392 1117 1130 100 12554 54 12500 .563 13121 13068 1.776 .56 -.829 -.838

Total number of rows: 24288

Table truncated, full table size 5453 Kbytes.




Supplementary file Size Download File type/resource
GSM498975.gpr.gz 2.1 Mb (ftp)(http) GPR
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap