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Sample GSM3821 Query DataSets for GSM3821
Status Public on Feb 05, 2003
Title Overexpression of the plant LAMMER kinase PK12 b90
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 -0.0447933 6100.5 2486.642822 1167.566772 2310.853027 103.109421 1200 47.510372 0.861381 0.971596 0.922997 2.639934 0.703982 11187.88867 4033.857178 2096.146973 2639.454346 68.636635 900 47.510372 0.69526 0.960876 0.927864 4.238713 0.618009 1 0.902
2 -0.0347983 6908.6875 2957.714355 1592.202637 2279.313232 99.014877 1600 31.183199 0.878694 0.94854 0.934532 3.031039 0.781062 13713.14258 5710.446289 2692.2854 3126.814209 78.176407 700 31.183199 0.698331 0.942093 0.905418 4.38566 0.620739 1 0.923
3 0.1166083 6941.179688 2613.321533 2197.926025 2074.306152 111.132469 3900 38.980732 0.937607 0.932243 0.936737 3.346266 0.812954 17909.06641 5479.535645 13276.72168 2879.212158 89.206215 1500 38.980732 0.829499 0.593567 0.920135 6.220127 0.527615 1 1.308
4 0.2247923 6132.350098 2163.928467 2693.526123 1943.127197 99.335838 2000 38.126987 0.794983 0.937027 0.951218 3.155918 0.706652 19606.05859 4992.856934 13594.55078 2804.691162 88.848671 1700 38.126987 0.859256 0.638634 0.917213 6.990452 0.567674 1 1.678
5 -0.0181813 5156.222168 2050.25 1096.672363 1702.179199 105.248215 1800 39.139561 0.889626 0.966797 0.956276 3.029189 0.790779 11253.5 4714.785645 2870.665771 2747.154541 41.459301 400 39.139561 0.364833 0.952843 0.921761 4.09642 0.324296 1 0.959
6 -0.1890963 5229.111328 2207.785645 707.521118 1868.212646 82.533829 900 40.825825 0.67634 0.984497 0.956276 2.798992 0.601191 8349.384766 4057.982178 720.246338 2620.903809 96.078033 1300 40.825825 0.768015 0.983032 0.930229 3.185689 0.68268 1 0.647
7 -0.0419143 4332.333496 1487.517822 1674.963379 1363.846436 124.121719 4200 39.308167 0.933647 0.934944 0.962234 3.176555 0.806821 8691.645508 3021.607178 1775.43689 2471.497314 113.681061 3100 39.308167 0.891842 0.946457 0.93605 3.516753 0.792749 1 0.908
8 -0.0181813 3676 1252.607178 1338.522339 1364.223267 122.3134 5000 38.305618 0.94582 0.957573 0.96492 2.694574 0.718553 7274.277832 2172.821533 2490.785156 1713.437012 118.882133 3600 38.305618 0.932889 0.917397 0.956467 4.245431 0.834793 1 0.959
9 -0.0414363 4002.461426 1493.982178 1155.78479 1713.702759 118.076141 5200 39.486427 0.910504 0.968437 0.948196 2.335563 0.622817 7465.827637 2461.821533 2289.677246 1970.429688 118.614082 2900 39.486427 0.909275 0.946449 0.9496 3.788934 0.818551 1 0.909
10 0.0417873 2877.04834 1204.517822 2820.510986 1678.548828 124.121719 6200 32.417583 0.954189 0.959999 0.957603 1.714009 0.457069 6484.620605 2442.910645 1286.544189 2106.269043 103.725006 2900 32.417583 0.899256 0.963776 0.935562 3.078724 0.799338 1 1.101
11 0.1562463 3016.285645 874.571411 1771.315308 1125.279419 126.911324 9800 21.460703 0.945656 0.94165 0.966553 2.680477 0.714794 9447.058594 2708.517822 6513.338379 2258.346924 102.800247 3400 21.460703 0.847058 0.764732 0.926125 4.183174 0.679762 1 1.433
12 0.0640833 3249.291748 1260.178589 1396.380249 1389.202881 120.477936 4800 19.255369 0.92804 0.955093 0.965034 2.338961 0.623723 7988.04541 2927.053467 2245.177979 1955.3125 103.417671 2200 19.255369 0.857685 0.949104 0.948143 4.085304 0.762386 1 1.159
13 0.0220163 4258.361328 1939.571411 2353.590332 2984.634521 110.269852 3600 39.871391 0.893014 0.929321 0.939552 1.426761 0.38047 8763.599609 3411.482178 5981.747559 4469.487305 110.558136 2500 39.871391 0.879282 0.777618 0.908279 1.960762 0.52287 1 1.052
14 -0.0824943 4230.143066 1460.142822 2043.832642 1534.742554 110.84568 2800 28.934477 0.86819 0.926811 0.957329 2.756256 0.735002 7588.947266 2560 2351.055664 2140.654053 96.408768 1900 28.934477 0.825515 0.930153 0.936745 3.545154 0.733791 1 0.827
15 -0.0830203 2630.743652 922.214294 1345.627197 843.35614 119.14959 3900 36.24577 0.934262 0.956497 0.981674 3.119375 0.804664 5343 2246.571533 1726.312256 1917.058228 113.681061 4000 36.24577 0.887596 0.929298 0.954063 2.787083 0.743222 1 0.826
16 0.2695133 2064.29126 840.75 1447.133301 1227.041016 127.910637 7900 38.787342 0.948451 0.956146 0.964622 1.682333 0.448622 7592.959961 2597.107178 2293.97583 2038.572876 105.550217 2500 38.787342 0.871225 0.94313 0.941612 3.724645 0.774422 1 1.86
17 -0.0680343 2910 955.321411 1298.32251 1068.673462 118.614082 4500 38.032738 0.96151 0.952354 0.972412 2.723002 0.726134 5295 1627.732178 1830.122192 1565.818604 120.741859 4300 38.032738 0.941957 0.938034 0.95208 3.381618 0.814182 1 0.855
18 -0.3089193 3795.65918 1291.482178 2272.704346 2291.891846 118.882133 4400 42.417637 0.93892 0.930573 0.95623 1.656125 0.441633 5883.15625 3181.589355 2410.953369 7144.390137 116.992851 3200 42.417637 0.936606 0.929619 0.818306 0.823465 0.219591 1 0.491
19 -0.1844223 3694.507813 1313.446411 1964.610962 1561.24939 117.806259 6500 40.517857 0.93909 0.940201 0.960899 2.366379 0.631034 5682.022461 2262.321533 1631.703003 2030.76416 118.345421 4500 40.517857 0.933058 0.948837 0.94915 2.797973 0.746126 1 0.654
20 -0.1209043 3172.524902 1257.982178 1037.128296 1324.099121 122.573364 4000 42.710747 0.941896 0.968803 0.965279 2.395987 0.63893 4975.316895 1795.25 2483.851318 1730.805176 118.882133 6000 42.710747 0.937195 0.950195 0.948608 2.874568 0.766551 1 0.757

Total number of rows: 8826

Table truncated, full table size 2204 Kbytes.




Supplementary data files not provided
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