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Sample GSM3822 Query DataSets for GSM3822
Status Public on Feb 05, 2003
Title Overexpression of the plant LAMMER kinase PK12 t100
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 -0.1674913 9182.799805 3949.696533 3764.328125 3402.280762 109.400429 2500 55.95327 0.881318 0.875259 0.916878 2.699013 0.719737 6386.516113 3202.875 2030.797119 3567.959473 113.119675 3100 55.95327 0.895932 0.930878 0.922523 1.789963 0.477324 1 0.68
2 -0.1408623 10883.31445 3578.446533 3391.081787 3028.59082 124.121719 5400 45.372845 0.933265 0.901566 0.913116 3.593524 0.785477 7499.619629 2775.446533 3205.646729 3581.205566 118.882133 7100 45.372845 0.920325 0.904625 0.910576 2.094161 0.558443 1 0.723
3 -0.0428723 10225.44922 2971.089355 4886.0625 2801.700928 119.682693 6900 42.283104 0.926768 0.848221 0.922394 3.649729 0.753974 9131.830078 3246.535645 3855.588135 3411.735596 118.614082 5300 42.283104 0.901746 0.882225 0.897575 2.676594 0.713758 1 0.906
4 -0.0150233 9855.791992 3548.964355 2885.813965 3253.359131 110.558136 5300 34.964615 0.904021 0.912888 0.91275 3.02942 0.785161 8124.377441 2673.035645 3465.590576 2749.197266 112.272324 5300 34.964615 0.907553 0.89595 0.917252 2.955182 0.788048 1 0.966
5 -0.0282603 8995.176758 3052.625 3424.829346 2783.394531 126.911324 7900 35.56514 0.941813 0.895233 0.930672 3.231729 0.795763 7402.078613 2415.428467 3866.706543 2998.105469 126.156639 8900 35.56514 0.941346 0.884422 0.928154 2.468919 0.658378 1 0.937
6 -0.2020403 13807.93359 4279.428711 5541.734863 3566.167969 81.368584 1500 46.264462 0.867215 0.862137 0.889862 3.871925 0.765473 7838.06543 2483.089355 2544.914551 2110.265381 121.005196 4600 46.264462 0.915251 0.906509 0.949402 3.714256 0.813019 1 0.628
7 -0.0385793 10355.43555 3824.482178 3864.369141 2765.233643 115.624466 3900 50.150696 0.88634 0.855713 0.92878 3.744868 0.760634 8394.276367 3044.589355 3502.07373 2725.888916 113.400711 4700 50.150696 0.877191 0.880508 0.927872 3.079464 0.779726 1 0.915
8 -0.0141253 9646.5 3647.678467 3501.317627 3916.143799 117.264618 5400 40.311878 0.904734 0.901337 0.876518 2.463265 0.656871 7622.333496 2422.053467 3428.304932 2516.047119 118.076141 7200 40.311878 0.923989 0.886887 0.930458 3.029488 0.788344 1 0.968
9 -0.0218193 9537.345703 3820.178467 3705.077148 4470.880859 103.109421 5200 43.516388 0.904101 0.896652 0.876518 2.133214 0.568857 7971.467773 3102.446533 3011.318115 3134.188232 123.349976 6200 43.516388 0.94353 0.901169 0.914757 2.543392 0.678238 1 0.951
10 -0.0793553 9347.651367 3542.571533 2836.27417 3889.175293 116.992851 4300 40.603874 0.919272 0.915138 0.931732 2.403505 0.640935 6399.296875 2069.5 2905.043701 2057.606201 125.143318 6400 40.603874 0.947319 0.909424 0.936859 3.110069 0.804308 1 0.833
11 -0.0867163 10330.63672 4323.196289 3018.506836 3576.851563 118.345421 2200 34.122868 0.889873 0.922401 0.900558 2.888193 0.770185 6677.759277 2272.607178 3508.832275 2777.440674 120.21344 5400 34.122868 0.911247 0.91037 0.943329 2.404285 0.641143 1 0.819
12 -0.0963673 11116.28613 4114.196289 4065.977295 3284.713135 108.230339 2800 27.067547 0.855817 0.851105 0.899345 3.384249 0.756538 7183.051758 2162.321533 4131.179199 2916.16333 124.121719 5800 27.067547 0.916339 0.87426 0.934402 2.463186 0.65685 1 0.801
13 -0.0695603 12533.23828 4291.143066 4528.358887 3128.92749 111.418526 6300 41.825298 0.909456 0.87883 0.90329 4.005602 0.777023 8617.222656 2332.767822 3270.57373 2015.106079 111.988449 5400 41.825298 0.914393 0.908272 0.937057 4.276312 0.816544 1 0.852
14 -0.2941363 12849.78027 4955.018066 3482.619385 4021.371094 115.072563 4100 37.400177 0.908375 0.88945 0.897911 3.195373 0.772397 6435.426758 2845.839355 2879.587402 3283.042969 128.902206 8200 37.400177 0.948007 0.92038 0.909592 1.960202 0.52272 1 0.508
15 -0.2941363 13462.86621 5049.125 3908.355225 4188.407227 111.418526 3000 42.434708 0.913625 0.868774 0.884682 3.214316 0.761016 6015.403809 2186.071533 3197.190918 3056.695557 127.411957 10400 42.434708 0.958897 0.900452 0.905876 1.967943 0.524785 1 0.508
16 -0.2232993 14405.84863 4558.571289 5948.794922 3633.302002 89.91703 3300 51.153439 0.864067 0.789017 0.901199 3.964947 0.701348 7623.224121 2350.75 2846.515137 2625.353516 121.530167 6700 51.153439 0.931301 0.923035 0.920937 2.903694 0.774319 1 0.598
17 -0.2034263 12232.6543 4408.893066 4681.858887 3458.510498 96.408768 2600 38.584942 0.829432 0.862511 0.909103 3.536972 0.737273 6733.793457 2353.357178 3112.040039 2836.47998 120.741859 6300 38.584942 0.928038 0.918892 0.93103 2.373996 0.633066 1 0.626
18 -0.1450873 12832.90039 4057.464355 4338.929199 3440.667725 100.292542 5000 42.985386 0.859042 0.866577 0.910782 3.72977 0.763592 8626.807617 3005.089355 3097.160645 3471.444092 115.072563 5200 42.985386 0.918035 0.914619 0.899841 2.485078 0.662687 1 0.716
19 -0.1163393 12251.5 4403.106934 3110.527344 3993.848633 92.016548 2200 39.102238 0.745429 0.922707 0.905869 3.067592 0.662604 8803.709961 3426.642822 3479.726074 3421.848145 120.477936 3100 39.102238 0.922199 0.873222 0.908646 2.572794 0.686078 1 0.765
20 -0.0390543 11710.5166 4278.428711 3844.989014 3729.748535 107.344398 3100 33.616165 0.928401 0.850845 0.890839 3.13976 0.756307 9067.811523 2986.339355 2895.108643 2542.658691 119.416435 5300 33.616165 0.939783 0.92263 0.932114 3.566272 0.806039 1 0.914

Total number of rows: 8829

Table truncated, full table size 2211 Kbytes.




Supplementary data files not provided
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