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Sample GSM3820 Query DataSets for GSM3820
Status Public on Feb 05, 2003
Title Overexpression of the plant LAMMER kinase PK12 b100
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 -0.0118873 3833.741943 1148.785767 2663.427734 1492.036377 125.651001 6200 46.63649 0.954058 0.924789 0.961472 2.569469 0.685192 22999 7506.106934 354.96759 4728.303223 0 200 46.63649 0 0.99617 0.864082 4.864113 0 1 0.973
2 -0.1186153 6128.793457 1441.285767 3576.041504 1589.579468 117.264618 6300 49.134747 0.887012 0.900574 0.958054 3.855607 0.788455 30106.69141 8944.875 10161.58496 4754.120117 85.934807 5500 49.134747 0.928769 0.734764 0.859436 6.332758 0.653124 1 0.761
3 -0.0259493 5243.529297 1637.660767 2922.918945 1987.552124 120.741859 6800 56.080223 0.922822 0.921547 0.949516 2.638185 0.703516 27954.4707 7797.125 9249.993164 4684.726563 94.069214 5100 56.080223 0.871942 0.779037 0.865623 5.967151 0.692478 1 0.942
4 -0.0931263 4896.875 1909.625 2392.876709 2361.384033 113.400711 4800 35.872585 0.914438 0.927406 0.933372 2.073731 0.552995 21396.27344 7099.143066 6194.613281 4829.333496 106.451088 6200 35.872585 0.900019 0.813766 0.868782 4.430482 0.723348 1 0.807
5 0.0145213 3961.481445 1401.071411 2858.419434 1831.557373 121.530167 8100 34.073147 0.943276 0.91613 0.950371 2.162903 0.576774 22188.12695 6483.518066 7836.699219 4249.712402 100.609428 6300 34.073147 0.880397 0.776848 0.876823 5.221089 0.690531 1 1.034
6 -0.0017413 4099.678223 1554.732178 2419.109131 2069.014648 129.886215 8700 45.2957 0.964516 0.938019 0.94812 1.981464 0.52839 21625.30273 6594.035645 5291.765137 4178.938965 87.403885 4300 45.2957 0.841855 0.839752 0.866081 5.174831 0.745016 1 0.996
7 -0.0560113 4354.506348 1346.785767 3138.195557 1695.801147 121.005196 7700 38.86573 0.951099 0.903893 0.958725 2.567817 0.684751 22447.43945 6758.785645 6969.467285 4714.917969 106.749687 5700 38.86573 0.894891 0.778786 0.866928 4.76094 0.692254 1 0.879
8 0.0000003 4869.700195 1948.946411 2527.604492 2230.859863 122.573364 7000 36.454029 0.944285 0.920197 0.932693 2.18288 0.582101 24007.38672 6689.928711 6500.172852 4468.193848 94.743553 6200 36.454029 0.872136 0.820541 0.872116 5.372951 0.72937 1 1
9 0.0689283 3991.822754 1432.464233 2971.573486 2399.734619 120.477936 7900 34.511623 0.929434 0.913406 0.931694 1.663443 0.443585 26025.87695 8227.357422 6057.191895 5072.909668 88.129242 4900 34.511623 0.880112 0.829575 0.866692 5.130365 0.7374 1 1.172
10 0.0874263 4157.634766 2127.571533 2033.983521 3033.403809 107.344398 5200 35.511276 0.842972 0.941269 0.913147 1.370617 0.365498 21467.78516 6735.856934 7198.373535 4384.485352 94.406982 4200 35.511276 0.850692 0.786621 0.8592 4.896307 0.699219 1 1.223
11 -0.1255183 5482.164063 1968.767822 3835.831543 2314.69165 119.948364 6100 34.746475 0.921277 0.910568 0.932777 2.368421 0.631579 23845.19922 8245.232422 5587.248047 5192.549805 92.016548 3500 34.746475 0.91311 0.854477 0.859383 4.592195 0.739254 1 0.749
12 -0.0974533 4781.862793 1900.821411 2545.4104 2520.176514 120.741859 5100 46.026817 0.934124 0.931053 0.932777 1.897432 0.505982 21236.65625 7581.481934 4730.512207 5017.708008 108.230339 3500 46.026817 0.883677 0.848381 0.853485 4.232342 0.734181 1 0.799
13 -0.0690513 4765.605469 1347.982178 2457.461914 1872.150024 125.397415 7100 34.991455 0.947221 0.935844 0.946991 2.545525 0.678807 25089.45703 7798.589355 7422.398926 4358.344238 85.563599 3500 34.991455 0.847174 0.804482 0.884041 5.756649 0.715095 1 0.853
14 -0.0665133 4245.875 1320.839233 2804.40625 1925.693848 125.143318 7200 46.28566 0.926468 0.916374 0.953835 2.204855 0.587961 22204.58789 7310.356934 6925.986328 4940.245117 96.078033 4600 46.28566 0.866007 0.733719 0.863548 4.494633 0.652195 1 0.858
15 0.0021663 4090.442871 1286.089233 2389.337158 1615.559204 126.660263 7000 26.420919 0.96101 0.930756 0.950104 2.531905 0.675175 24662.61523 7949.160645 6223.303711 4356.128418 94.406982 3900 26.420919 0.825552 0.823936 0.857574 5.66159 0.732388 1 1.005
16 -0.1830963 4523.40332 1314.678589 2235.293945 1717.340332 118.614082 6200 46.551861 0.914993 0.947174 0.958405 2.633959 0.702389 18973.72461 6494.356934 6162.64209 4541.48584 112.272324 5800 46.551861 0.904597 0.827507 0.879005 4.177867 0.735562 1 0.656
17 -0.0476923 3870.357178 1244.464233 2486.736084 1696.56543 119.14959 7000 35.510967 0.944857 0.926804 0.962868 2.28129 0.608344 20314.73828 6358.946289 6686.543945 4530.46582 109.109085 4600 35.510967 0.89648 0.793076 0.879875 4.484029 0.704956 1 0.896
18 -0.0752043 3189.241699 911.571411 2596.39209 1270.56311 120.477936 9100 38.057426 0.937665 0.902412 0.967758 2.510101 0.66936 15964.79199 4600.035645 6790.427246 3671.573486 110.269852 7700 38.057426 0.909724 0.786491 0.883141 4.348215 0.699103 1 0.841
19 -0.0254883 3512.289063 912.892883 2874.298096 1424.103149 125.904076 8300 54.489014 0.928524 0.903862 0.95507 2.466316 0.657684 21187.32422 6641.481934 7097.54834 4101.304688 115.899437 6800 54.489014 0.91053 0.787109 0.87674 5.165996 0.699653 1 0.943
20 -0.0809223 4029.028076 1274.589233 2594.034912 2247.689941 118.882133 7100 38.402081 0.931644 0.922951 0.921494 1.79252 0.478005 21393.05469 7828.089355 5102.257324 4349.349609 93.048538 3600 38.402081 0.774725 0.825127 0.855499 4.918679 0.688645 1 0.83

Total number of rows: 8829

Table truncated, full table size 2212 Kbytes.




Supplementary data files not provided
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