Description Usage Details Source Examples
LR_dataset is a matrix of dimension 15240 lines x 18 columns. It stores a time-series transcriptomic dataset following the changes occuring in a young Arabidopsis root during the formation of a lateral root. To generate this dataset, lateral root formation was locally induced by a gravistimulus at t=0 and the stimulated part of the roots was collected every 3 hours from 6 hours to 54 hours. The transcriptomes were analyzed using the ATH1 affymetrix chip. For time point 0, unstimulated young primary root was taken as a control. Importantly, the transcript accumulation levels stored in this dataset are non-log2 values.
1 | data("LR_dataset")
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The experiment spanned 54 hours in order to cover all aspects of lateral root development. Using this method,
lateral root initiation (the first pericycle divisions) occurs synchroneously in all stimulated roots around 12 hours after stimulation
and the fully formed lateral root emerges from the parental root around 45 hours. The dataset contains data for all significantly differentially
expressed genes.
Each column is the average of 4 independent replicates. The columns are organized in the following order: 0, 6, 9, 12, 15, 18, 21, 24, 27, 30, 33, 36, 39, 42, 45, 48, 51 and 54 hours. Each line of the matrix is labbelled with an AGI gene code (Arabidopsis Genome Initiative gene code).
Voss et al., Lateral root organ initiation re-phases the circadian clock in Arabidopsis thaliana. Nature communication, in revision.
1 2 3 4 5 | # Load the dataset
data(LR_dataset)
# Have a look at the first rows
head(LR_dataset)
|
Loading required package: deSolve
V1 V2 V3 V4 V5 V6
AT1G01010 225.97197 202.25058 190.01902 178.5272 188.70646 205.07389
AT1G01040 133.43562 156.49796 154.34340 136.2394 160.89771 139.10206
AT1G01050 879.17101 786.88009 891.44378 975.5013 1002.92638 1009.90229
AT1G01060 43.41134 39.67065 64.44516 192.6716 398.93226 458.25284
AT1G01070 643.59085 541.19324 533.74247 451.9439 467.88170 448.82213
AT1G01080 55.33038 58.48521 64.00000 61.3929 60.12946 60.96883
V7 V8 V9 V10 V11 V12
AT1G01010 230.72012 215.2695 184.82294 172.44590 199.46613 222.86094
AT1G01040 135.29831 130.6896 117.78402 100.42676 116.97043 115.36006
AT1G01050 1002.92638 1074.9099 1128.35084 1089.91507 1160.07310 1120.55675
AT1G01060 448.82213 250.7316 91.13921 26.53823 36.00187 119.42822
AT1G01070 464.64981 504.9511 410.14778 276.28243 233.94085 230.72012
AT1G01080 60.12946 54.1917 56.10277 50.91433 50.21338 45.25483
V13 V14 V15 V16 V17 V18
AT1G01010 238.8564 225.97197 207.93661 128.89031 114.56321 108.38340
AT1G01040 113.7719 112.20553 109.13727 103.25015 92.41147 95.00951
AT1G01050 1120.5568 1128.35084 1144.10203 1184.44870 1168.14205 1234.74722
AT1G01060 247.2797 284.04978 210.83930 123.63985 89.26359 54.56863
AT1G01070 200.8535 188.70646 229.12642 187.40297 159.78631 162.01684
AT1G01080 44.6318 53.07645 49.52208 44.94224 39.39662 37.27147
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