LR_dataset: Lateral root transcriptomic dataset

In TDCor: Gene Network Inference from Time-Series Transcriptomic Data

Description

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.

Usage

data("LR_dataset")

Details

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).

Source

Voss et al., Lateral root organ initiation re-phases the circadian clock in Arabidopsis thaliana. Nature communication, in revision.

Examples

# Load the dataset
data(LR_dataset)

# Have a look at the first rows
head(LR_dataset)

Example output

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

TDCor documentation built on May 2, 2019, 3:41 p.m.