Space and epigenetic inheritance determine inter-individual differences in siderophore gene expression in bacterial colonies

This project contains all the data and custom code used in Mridha et al. (2024), Space and epigenetic inheritance determine inter-individual differences in siderophore gene expression in bacterial colonies.
Mridha_et_al_2024_CellReports_raw_data.xlsxOverview of the figures, data descriptions and raw data for all figuresimage_analysiscode:make_avg_blank.py: Creates average projection images for each channel of a multichannel image stack and saves them as separate TIFF filesblank_subtraction.py: Subtracts an averaged blank from the currently opened image to correct for image vignettingimage_measurments.py: Measures single cells in several channels, with a provided single cell segmentationdata_analysiscode:
process_results.R: Clusters cells into colonies and calculates the distance of each cell to the edge of a colonylineage_mean.R: Calculates lifespan and average gene expression among other metrics for individual cellsF1_Patterns_of_gene_expression.R: Analysis for figure 1F2_Spatial_Gradients.R: Analysis for figure 2F3_Lifespan_Gene_Expression.R: Analysis for figure 1F4_Poleage.R: Analysis for figure 4F5_Lineage.R: Analysis for figure 5FS3.R: Analysis for figure S3FS4.R: Analysis for figure S4FS5.R: Analysis for figure S5data:
single_cell_data.csv: Single cell and colony level datalineage_data.csv: Single cell and lineage datamean_lineage_data.csv: Single cell and lineage data averages per single cellF1_a_d.csv: Siderophore gene expression average per colony and time-pointF1_a_d_mean.csv: Siderophore gene expression average per time-pointF1_b_e.csv: Siderophore gene expression average per colonyF1_c_f.csv: Temporal changes in siderophore gene expressionF1_g.csv: Siderophore gene expression correlation per colony and time-pointF1_g_mean.csv: Siderophore gene expression correlation per time-pointF1_h.csv: Siderophore gene expression correlation per colonyF1_i.csv: Temporal changes in Siderophore gene expression correlationF2_b.csv: Spatial correlation of Siderophore gene expression within coloniesF3_a_b.csv: Siderophore gene expression and lifespan example positionF3_c_d.csv: Partial correlation between siderophore gene expression and lifespan F4_a_b.csv: Pole age and siderophore gene expressionF5_a.csv: Differences in PVD gene expression between sisters and neighboursF5_b.csv: Differences in PCH gene expression between sisters and neighboursF5_c_d.csv: Lineage effects on siderophore gene expressionFS4_a_b.csv: Correlations between colony fitness and cellular heterogeneityFS5_a.csv: DeLTA pipeline segmentation accuracy