This repository contains the quantified data and processing scripts (MATLAB) of literature "Temporal analysis of mammalian genetic circuits using multiplexed transcriptional imaging".
The figure_scripts folder contains the scripts for create figure from the data. Other folders contains quantified data and processing scripts of different datasets, except the data generated by simulation, which could be generated by running the simulation scripts. The datasets in those folders are listed below:
single_barcode_transient: the dataset of the cells with five transient transfected single barcode respectively
single_barcode: the dataset of the cells with five stable transfected single barcode respectively
double_barcode: the dataset of the cells with double barcode of 1:0/0:1 or 1:2/2:1
ABC: the dataset of the cells with the synthetic three-gene cascade circuit
ABCDE: the dataset of the cells with the five-gene branched cascade circuit
ABC_simulation: the simulation results corresponding to the synthetic three-gene cascade circuit
The mat files in these folders are the quantified data generated by quantified software and manually classification, recording the infomations including mitosis time of cell, the fluorescent inthensity of the gene loci and a description about the detail informations of the dataset. The data are restored as four level: cell_set, cell, spot_set and spot. Cell_sets are sets of cells that were collected under the same condition. Cells are the data of every single cells, including the mitosis time of the cell and several spot_sets. Spot_sets contains spots that classified as the same group, usually by ratio of the fluorescent intensity. Spots represent the fluorescent spots form by transcription reporters in the cells, namely, the gene loci that were transcribing mRNAs. A spot record contain the intensity of CFP and mCherry fluorscence along time.
The MATLAB scripts (filename.m) are used to process the data and to add more processed informations about bursts, regulation, etc. into the datasets. Every folders have a total_workflow.m as guidence of the using of these scripts. Directly running total_workflow.m would finish all the processing.
What's more, a json file is provided in every folders, these json files contains all processed data of the datasets. Users have no access to MATLAB can read this file with any other language or online/local json reader, for json is a common storage format. These files were encoded with UTF-8.