code and data in support of the fucci paper
=== Section 1: Processing microscopy data === Data processing workflow is as follows: Sample preparation --> Filming --> Automated selection of single cell wells --> Manual annotation --> Input tables --> Data analysis.
This section describes the last step. The input for this step is contained in files listed below. Each file corresponds to one experiment. Note that '20111118', '20120309', and '20120316' have a slightly different table format from '20120413', but this fact is taken care of during importing. In these tables and derived data structures, times are measured in hours.
data/ 20111118_division_data.csv 20120309_division_data.csv 20120316_division_data.csv 20120413_division_data.csv
Script [runImportAnnotated.m] reads the *.csv files and yields Matlab data files for convenience of further processing. Note that this script imports one file at a time. To choose a different *.csv input, uncomment the corresponding line (lines 12--15, e.g., "par.sExpName = '20111118'; ..."). The script discards any inconsistent annotations by comparing event timings for individual cells (e.g., the cell is discarded if time to green off is earlier than time to green on). The output of the script is as follows.
data/ 20111118-cycle-meas.mat 20120309-cycle-meas.mat 20120316-cycle-meas.mat 20120413-cycle-meas.mat
Script [runProcessFucciData.m] is then processes data, produces figures and prints some statistics. This script also produces intermediate data files.
data/ 20111118-info.mat 20120309-info.mat 20120316-info.mat 20120413-info.mat
Scripts [runBootstrapParamsS1.m], [runBootstrapParamsS3.m] and [runBootstrapParamsS3_v2] produce bootstrapped confidence intervals for parameters from Supplementary Tables S1 amd S3. The difference between [*S3.m] and [*S3_v2.m] is that the former uses a complete dataset for each condition, whereas the latter uses a set of randomly chosen siblings from all sibling pairs for each condition. Table S3 presetned in the paper is generated using [*S3_v2.m]. Together these 3 scripts create files:
data/ boundsS1.mat boundsS3.mat boundsS3_v2.mat
... as well as these auxiliary files: data/ bounds.mat moments.mat
Script [runBoundsVSMoments.m] compares estimated bounds from [data/bounds.mat] to estimated parameters of EMG recorded in [data/moments.mat]. This script is not used in the current version of the paper.
Script [runBootstrapParamsS2.m] produces bootstrapped confidence intervals for parameters from Supplementary Table S2. The intervals are printed in the console.
Script [runTotDivDist.m] fits various distributions (e.g., lognormal, gamma, Weibull) to data.
=== Section 2: Processing FACS data === File "data/SH1.93 G2M summary.xlsx" contains gated FACS results from the BrdU treatment experiment. "All in division" tab contains results for a dividing population (i.e., undivided cells are excluded). In this tab, the numbers are percentages out of total number of live dividing cells. For each gate, columns show triplicates.
Script [runStretchedG2M.m] reads this data file (and saves data structures in an intermediate file named "data/BrdU-data.mat"), fits the stretched G2M model to the data, and produces figures.
=== Legal stuff === Copyright (c) 2013 The Walter & Eliza Hall Institute of Medical Research
This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0.
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