NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3823 Query DataSets for GSM3823
Status Public on Feb 05, 2003
Title Overexpression of the plant LAMMER kinase PK12 t90
Sample type RNA
 
Channel 1
Source name Non-transformed plants
Organism Arabidopsis thaliana
Extracted molecule total RNA
 
Channel 2
Source name Plants that overexpress PK12
Organism Arabidopsis thaliana
Extracted molecule total RNA
 
 
Description RNA was extracted from plants that overexpress PK12 and from non-transformed plants. Plants were grown for 21 days under long day conditions. Hybridization was performed on an array from Arabidopsis Keck Resource Lab Array (Yale University) containing 9K Arabidopsis ESTs. Data in this platform contains 4 repetitions including 2 independent biological experiments.
Keywords = alternative splicing, phosphorylation
 
Submission date Feb 02, 2003
Last update date May 27, 2005
Contact name Robert Fluhr
E-mail(s) robert.fluhr@weizmann.ac.il
Phone 972-8-9342175
Organization name Weizmann Institute of Science
Department Plant Sciences
Street address
City Rehovot
ZIP/Postal code 76100
Country Israel
 
Platform ID GPL243
Series (1)
GSE274 Overexpression of the plant LAMMER kinase PK12

Data table header descriptions
ID_REF
VALUE log ratio of PRE_VALUE
ch1 Intensity Channel 1 average (mean) of intensities
ch1 Background Channel1 background
ch1 Intensity Std Dev Channel 1 Intensity standard deviation
ch1 Background Std Dev Channel 1 background standard deviation
ch1 Diameter Channel 1 diameter of the spot
ch1 Area Number of pixels used when calculating spot intensity
ch1 Footprint Channel 1 distance between the expect position of a spot and its actual measurment position
ch1 Circularity The degree to which a spot matches a perfect circle in channel 1
ch1 Spot Uniformity The uniformity of pixels used in the spot intensity calculation in channel 1
ch1 Bkg. Uniformity The uniformity of pixels used in the local background intensity calculation in channel 1
ch1 Signal Noise Ratio The ratio of the spot intensity to the standart deviation of the local background of all spots
ch1 Confidence channel1 Confidence
ch2 Intensity Channel 2 average (mean) of intensities
ch2 Background Channel2 background
ch2 Intensity Std Dev Channel 2 Intensity standard deviation
ch2 Background Std Dev Channel 2 background standard deviation
ch2 Diameter Channel 2 diameter of the spot
ch2 Area Number of pixels used when calculating spot intensity
ch2 Footprint Channel 2 distance between the expect position of a spot and its actual measurment position
ch2 Circularity The degree to which a spot matches a perfect circle in channel 2
ch2 Spot Uniformity The uniformity of pixels used in the spot intensity calculation in channel 2
ch2 Bkg. Uniformity The uniformity of pixels used in the local background intensity calculation in channel 2
ch2 Signal Noise Ratio The ratio of the spot intensity to the standart deviation of the local background of all spots
ch2 Confidence channel2 Confidence
Ignore Filter Ignore Filter
PRE_VALUE Each gene's measured intensity was divided by its control channel value in each sample. When the control channel value was below 10.0 the data point was considered bad. The 50th percentile of all measurements was used as a positive control for each sample. Each measurement for each gene was divided by this synthetic positive control, assuming that this was at least 0.01. The bottom tenth percentile was used as a test for correct background subtraction.

Data table
ID_REF VALUE ch1 Intensity ch1 Background ch1 Intensity Std Dev ch1 Background Std Dev ch1 Diameter ch1 Area ch1 Footprint ch1 Circularity ch1 Spot Uniformity ch1 Bkg. Uniformity ch1 Signal Noise Ratio ch1 Confidence ch2 Intensity ch2 Background ch2 Intensity Std Dev ch2 Background Std Dev ch2 Diameter ch2 Area ch2 Footprint ch2 Circularity ch2 Spot Uniformity ch2 Bkg. Uniformity ch2 Signal Noise Ratio ch2 Confidence Ignore Filter PRE_VALUE
1 -0.0736583 5637.25 2248.5 1188.930786 1715.935059 113.681061 2400 41.295399 0.892347 0.968651 0.952156 3.285235 0.793197 15215.57129 6831.196289 1457.004395 3137.334473 77.768173 700 41.295399 0.624217 0.966988 0.910332 4.84984 0.55486 1 0.844
2 -0.1284273 5920.714355 2370.25 1522.849121 1539.203125 111.418526 1400 44.294693 0.886386 0.958488 0.961868 3.84661 0.787899 13816.5 6071.089355 1320.168335 3327.401855 0 200 44.294693 0 0.985756 0.887634 4.152339 0 1 0.744
3 -0.0525663 5880.428711 2112.25 1172.940918 1629.635986 120.21344 2100 47.566105 0.922338 0.972847 0.959602 3.608431 0.820294 15451.09961 5656.143066 3075.971436 3260.005127 76.530403 1000 47.566105 0.608158 0.932419 0.905861 4.739594 0.540585 1 0.886
4 -0.3316143 7157.375 2339.625 1270.389038 1643.509888 97.066856 800 43.867161 0.857893 0.972839 0.94754 4.354933 0.762571 11905.22266 5323.143066 1772.385132 2866.137207 101.554138 900 43.867161 0.773235 0.963707 0.921783 4.153752 0.68732 1 0.466
5 0.0707763 4821.8125 2129.464355 719.880859 1846.814209 107.640526 1600 47.104687 0.843379 0.983696 0.946289 2.610881 0.696235 14892 5601.285645 0 2970.734375 0 100 47.104687 1 1 0.90937 5.012902 0.5 1 1.177
6 -0.1018243 5898 1860.267822 2832.279541 1941.344116 112.555481 1700 43.444847 0.898812 0.913635 0.94265 3.038101 0.798944 15214 5847.696289 1325.992432 2585.12207 25.231327 300 43.444847 0.141801 0.980804 0.913345 5.885215 0.126046 1 0.791
7 -0.0899093 4828.361328 1996.910767 1333.69458 1870.269897 113.681061 3600 46.647488 0.94051 0.948212 0.952454 2.581639 0.688437 13473.7002 6725.625 669.285217 3903.29834 89.206215 1000 46.647488 0.752464 0.985641 0.893509 3.451876 0.668857 1 0.813
8 -0.0052433 4428.866699 1665.357178 1316.287842 1609.676147 121.791801 3000 43.027912 0.936083 0.948761 0.958504 2.751402 0.733707 14099.55566 6094.696289 3392.649414 4035.024902 95.078926 900 43.027912 0.76844 0.916634 0.89109 3.494292 0.683058 1 0.988
9 0.0094513 4895.692383 2042.803589 1319.319214 1925.052368 119.948364 2600 46.19463 0.927769 0.965355 0.944229 2.543148 0.678173 14241.33301 5689.321289 2871.290283 2950.150879 91.322075 1200 46.19463 0.769628 0.934113 0.918648 4.827324 0.684114 1 1.022
10 -0.0665133 5263.035645 1976.982178 1908.066406 1881.373291 119.14959 2800 42.616508 0.936034 0.955162 0.944229 2.797444 0.745985 13453 5185.25 1625.322021 2771.954102 75.693985 500 42.616508 0.719479 0.970245 0.917847 4.853255 0.639537 1 0.858
11 0.1562463 3159.218262 1369.160767 1121.581665 1421.338135 118.882133 5500 45.746246 0.9061 0.970398 0.962776 2.222707 0.592722 12667.59961 5144.964355 3024.760498 2785.604248 89.562332 1000 45.746246 0.735852 0.924339 0.900734 4.547523 0.654091 1 1.433
12 0.0056093 3606.095215 1236.285767 1003.78009 1034.251099 111.70385 2100 42.2108 0.893034 0.97345 0.968094 3.486673 0.793808 12227.79981 5191.214355 1618.327148 2731.28125 79.788467 500 42.2108 0.756249 0.97049 0.919197 4.476946 0.672222 1 1.013
13 0.0330213 3438.785645 1177.107178 1507.060059 1156.715332 121.530167 5600 45.302464 0.963431 0.962776 0.970078 2.972888 0.79277 11759.16699 4602.25 1694.687988 2461.475586 101.867088 1200 45.302464 0.845753 0.957329 0.930214 4.777284 0.751781 1 1.079
14 -0.0510983 3935.130371 1369.696411 1318.638672 1213.50415 118.614082 2300 41.810951 0.887635 0.956818 0.970078 3.242783 0.789009 11009.06641 4318.393066 2085.557129 2889.250244 99.335838 1500 41.810951 0.847723 0.945511 0.909828 3.810354 0.753531 1 0.889
15 0.0021663 3455.490234 1313.196411 1269.431885 1297.660645 120.477936 5100 44.863426 0.940518 0.959679 0.964333 2.662861 0.710096 9891.160156 3579.267822 3714.514893 2143.067871 110.269852 2500 44.863426 0.872625 0.890831 0.937767 4.615421 0.775667 1 1.005
16 -0.0101053 3574.296387 1501.303589 966.234192 1725.373779 117.535744 2700 41.417133 0.937894 0.969582 0.961136 2.071607 0.552429 10112 4170.910645 924.196472 2388.796875 79.388519 800 41.417133 0.755258 0.976738 0.927628 4.233093 0.671341 1 0.977
17 0.0553783 2848.27124 1090.517822 1375.136108 1383.902466 122.832779 5900 44.429268 0.92685 0.963783 0.964897 2.058144 0.548839 9526.845703 3669.232178 1579.032471 2378.871826 98.369827 1300 44.429268 0.853981 0.963905 0.929642 4.004775 0.759094 1 1.136
18 0.1507563 2351.838623 849.035706 1288.24353 1151.952271 128.655029 6200 47.71106 0.945273 0.966507 0.973122 2.041611 0.54443 9991.5 3757.267822 2013.930908 2401.395996 79.388519 600 47.71106 0.736191 0.960007 0.922607 4.160705 0.654392 1 1.415
19 0.3330443 2758.055664 1167.892822 1287.057129 1842.177246 120.741859 3600 44.000134 0.913904 0.963806 0.963425 1.497172 0.399246 13680.5 3642.107178 7863.476563 2357.681396 68.636635 800 44.000134 0.65454 0.830696 0.922607 5.802523 0.581813 1 2.153
20 0.1003713 3652.666748 1770.446411 774.294922 1999.394165 93.730225 1500 47.248348 0.816627 0.976044 0.962639 1.826887 0.48717 11038 4084.571533 1829.616943 2994.403076 94.406982 500 47.248348 0.719748 0.971367 0.904884 3.68621 0.639776 1 1.26

Total number of rows: 8823

Table truncated, full table size 2181 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap