This readme file describes several data files containing the raw data behind the publication "Exposure to lysed bacteria can promote or inhibit growth of neighbouring live bacteria depending on local abiotic conditions". Each CSV file is named after the figure of which it contains the raw data. "Figure 1 & 3; Yield and CFU definitive" contains the data for both figure 1 and 3. Note that Figure 1 contains the data of the "100x" dilution treatment only. Figure 3 again contains this data as the "100x" treatment, but also includes the two other dilution levels. Column "Well" gives the corresponding well number on the used microplate Column "0hrs" gives the Optical Density reading at timepoint 0 Column "24hrs" gives the Optical Density reading at timepoint 24 Column "Delta_OD" gives the change in Optical Density over 24 hours, and is the value in "24hrs" - "0hrs" Column "Initial_CFU_mL" gives the Colony Forming Units per mL at timepoint 0 Column "Final_CFU_mL" gives the Colony Forming Units per mL at timepoint 24 Column "Medium" gives growth medium used (LB or M9) Column "Dilution" shows the size of dilution used for that well Column "DC" shows whether dead cells were added or not (Yes/No) "Figure 2; Different LB percentages" Column "Well" gives the corresponding well number on the used microplate Column "0hrs" gives the Optical Density reading at timepoint 0 Column "24hrs" gives the Optical Density reading at timepoint 24 Column "Delta_OD" gives the change in Optical Density over 24 hours, and is the value in "24hrs" - "0hrs" Column "DC" shows whether dead cells were added or not (Yes/No) Column "LB_perc" shows the the dilution of LB used in this well as a percentage (10,40,70 and 100 percent) "Figure 4; TP5 all genes for plot FDR flagged","Figure 4; TP6.5 all genes for plot FDR flagged" and "Figure 4; TP24 all genes for plot FDR flagged" contain the data for figure 4, and contain the data for the three oabes in figure 4 in this order Column "gene_name" gives the name of the gene Column "pValue" gives the statistical significance of the expression change detected as a p-value Column "fdr" gives the statistical significance of the expression change detected as a False Discovery Rate-adjusted p-value Column "log2 Ratio" gives the log2 expression difference of this gene (positive means expressed more in the presence of dead cells) Column "Motility associated (Goterms: GO:0071973 (bacterial-type flagellum-dependent cell motility) ;GO:0071978 (bacterial-type flagellum-dependent swarming motility);GO:0044780 (bacterial-type flagellum assembly) ;GO:0006935 (chemotaxis);GO:0044781 (bacterial-ty" shows whether this gene is associated with any of the GO-terms in the column description (Yes or blank) Column "Motility" shows whether this gene is associated with cellular motility according to the terms mentioned in the Materials and Methods of this publication (Yes or blank) "Figure 5; Keio strain mutant assays" Column "<>" gives the corresponding well number on the used microplate Column "0hrs" gives the Optical Density reading at timepoint 0 Column "24hrs" gives the Optical Density reading at timepoint 24 Column "DeltaOD" gives the change in Optical Density over 24 hours, and is the value in "24hrs" - "0hrs" Column "Strain" gives the strain present in this well; this is either the Wild-Type (WT) or an otherwise isogenic single gene knockout mutant of the names gene (SoxS, lrp, CheY, RpoS, fnr, FliA, hns, FlhC) Column "DC" shows whether dead cells were added or not (Yes/No) "Figure S1B; Swimming distance motility assays" Column "Plate" shows the plate and whether dead cells (DC#) of an LB (LB#) control were used as chemo attractant/repellant Column "Block" shows in which experimental block this measurement belongs to (Block 1 to 4) Column "Maximum_diameter" shows the largest possible diameter of the swimming halo (edge to edge) measurable on that plate in millimeter. Upper limit is 90. Column "Maximum_radius" shows the largest possible distance measurable of the edge of the inoculated colony in the middle of the plate to the edge of the swimming halo in mm. Column "Dead_Cells_Added" shows whether dead cells were added as chemo attractant/repellant "Figure S2; effect of filtration" Column "Well" gives the corresponding well number on the used microplate Column "0_hrs" gives the Optical Density reading at timepoint 0 Column "24_hrs" gives the Optical Density reading at timepoint 24 Column "Delta_OD" gives the change in Optical Density over 24 hours, and is the value in "24hrs" - "0hrs" Column "CFU_mL" gives the Colony Forming Units per mL at timepoint 24 Column "DC" shows whether dead cells were added or not (Yes/No) Column "Treatment" shows whether the dead cells/control medium were filtered (Filt), heated (Heat), sonicated and filtered (Sony_filt) or sonicated and heated (Sony_heat) Figure S3A; effect of diff amounts of dead cells Column "Well" gives the corresponding well number on the used microplate Column "OD_0" gives the Optical Density reading at timepoint 0 Column "OD_24" gives the Optical Density reading at timepoint 24 Column "Delta_OD" gives the change in Optical Density over 24 hours, and is the value in "OD_0" - "OD_24" Column "Medium" gives growth medium used (LB or M9) and whether the well contained a control Column "DC" shows whether dead cells were added or not (Yes/No) Column "DC_amount" shows how much dead cell suspension/control medium was used (150/50) Figure S3B composite document. This is a composite dataset comprised of data from several other sets, mentioned in the description of column "dataset" Column "Well" gives the corresponding well number on the used microplate Column "OD" gives the Optical Density reading at timepoint 24 Column "Delta_OD" gives the change in Optical Density over 24 hours Column "Strain" shows which E.coli strain was used in this well, and can be either MG1655 or BW21533 Column "dataset" shows to which dataset this datapoint belonged. Column "Amount" shows the amount of dead cells suspension/control medium was present in this datapoint Figure S4; phage-lysed cells. Column "Well" gives the corresponding well number on the used microplate Column "0_hours" gives the Optical Density reading at timepoint 0 Column "24_hours" gives the Optical Density reading at timepoint 24 Column "delta_OD" gives the change in Optical Density over 24 hours, and is the value in "24hours" - "0hours" Column "Lysate" shows whether dead cells (EC) or control medium (LB) was used Column "Lysis_type" shows whether the dead cells were sonicated (Sonicated) or lysed by T7 phage (T7) Figure Figure S5A;Heat-killed cells comparisons. note that only the wells without glucose were used for this panel Column "Well" gives the corresponding well number on the used microplate Column "0.hrs" gives the Optical Density reading at timepoint 0 Column "24.hrs" gives the Optical Density reading at timepoint 24 Column "Delta.OD" gives the change in Optical Density over 24 hours, and is the value in "24hrs" - "0hrs" Column "Glucose" shows whether glucose was added to the well (Yes or No) Column "Dead cells" shows whether dead cells were added, and in which medium they were prepared. Note that in this figure, only DC in M9 (DC M9) and control M9 (M9 M9) were used Figure S5B; Heat-killed cells comparisons. note that for this figure, whole growth curves were used instead of end point measurements Column "Sample" gives the corresponding well number on the used microplate Column "k" gives the maximal OD calculated by growthcurver based on 24 hours of growth Column "Medium" shows the medium used (LB or M9). Note that only LB data was used in this figure Column "Dead cells" shows whether dead cells were or control medium (Yes or No) Column "Resuspension" shows whether cell resuspended before of after cell lysis by heat (see materials and methods). For this figure, only values of "Before" were used Figure S5C; Heat-killed cells comparisons Column "sample" gives the corresponding well number on the used microplate Column "k" gives the maximal OD calculated by growthcurver based on 24 hours of growth Column "Medium" shows the medium used (LB or M9). Note that only LB data was used in this figure Column "Dead cells" shows whether dead cells were or control medium (Yes or No) Column "Sonicated" shows whether dead cells were sonicated or not Figure S6; heated and sonicated cells Column "Well" gives the corresponding well number on the used microplate Column "0_hrs" gives the Optical Density reading at timepoint 0 Column "24_hrs" gives the Optical Density reading at timepoint 24 Column "Delta_OD" gives the change in Optical Density over 24 hours, and is the value in "24hrs" - "0hrs" Column "CFU_mL" gives the Colony Forming Units per mL at timepoint 24 Column "DC" shows whether dead cells were added or not (Yes/No). Column "Treatment" shows whether the dead cells/control medium were, heat-treated (Heat), or sonicated and heat-treated (Sony_heat). Blanks were control wells without dead cells or control medium. Figure S8; M9 plus different C-sources Column "<>" gives the corresponding well number on the used microplate Column "0_hrs" gives the Optical Density reading at timepoint 0 Column "24_hrs" gives the Optical Density reading at timepoint 24 Column "Delta_OD" gives the change in Optical Density over 24 hours, and is the value in "24hrs" - "0hrs" Column "DC" shows whether dead cells were added or not (Yes/No) Column "Medium" shows what medium was present. In this experiment, 10% strength LB (10%_LB), M9 without carbon (M9), M9 with casamino acids (M9_CA), M9 with glucose (M9_glu), and M9 with glycerol (M9_gly) were used. Figure S9 & S10; Yield and CFU different inocula. Note that this is the same dataset as for figure 1 and 3 Column "Well" gives the corresponding well number on the used microplate Column "0hrs" gives the Optical Density reading at timepoint 0 Column "24hrs" gives the Optical Density reading at timepoint 24 Column "Delta_OD" gives the change in Optical Density over 24 hours, and is the value in "24hrs" - "0hrs" Column "Initial_CFU_mL" gives the Colony Forming Units per mL at timepoint 0 Column "Final_CFU_mL" gives the Colony Forming Units per mL at timepoint 24 Column "Medium" gives growth medium used (LB or M9) Column "Dilution" shows the size of dilution used for that well Column "DC" shows whether dead cells were added or not (Yes/No) Column "Start_CFU_5_before_dilution" shows the actual colony count on a 10^-5 dilution plate at time point 0 Column "Start_CFU_6_before_dilution" shows the actual colony count on a 10^-6 dilution plate at time point 0 Column "Final_CFU_2" shows the actual colony count on a 10^-2 dilution plate at time point 24. Note that "TMTC" stands for "Too Many To Count" Column "Final_CFU_3" shows the actual colony count on a 10^-3 dilution plate at time point 24. Note that "TMTC" stands for "Too Many To Count" Column "Final_CFU_4" shows the actual colony count on a 10^-4 dilution plate at time point 24. Note that "TMTC" stands for "Too Many To Count" Column "Final_CFU_5" shows the actual colony count on a 10^-5 dilution plate at time point 24. Note that "TMTC" stands for "Too Many To Count" Column "Final_CFU_6" shows the actual colony count on a 10^-6 dilution plate at time point 24. Note that "TMTC" stands for "Too Many To Count" Figure S11; mutants with different amounts of dead cells Column "Well" gives the corresponding well number on the used microplate Column "0_hrs" gives the Optical Density reading at timepoint 0 Column "24_hrs" gives the Optical Density reading at timepoint 24 Column "Delta_OD" gives the change in Optical Density over 24 hours, and is the value in "24hrs" - "0hrs" Column "Strain" gives the strain present in this well; this is either the Wild-Type (WT) or an otherwise isogenic single gene knockout mutant of the names gene (RpoS, FliA, FlhC) Column "DC" shows whether dead cells were added or not (Yes/No) Column "Amount" shows how much dead cell suspension was used (50 or 150 microliter) Figure S12; ASKA strain assays Column "<>" gives the corresponding well number on the used microplate Column "0hrs" gives the Optical Density reading at timepoint 0 Column "24 HRS" gives the Optical Density reading at timepoint 24 Column "Delta_OD" gives the change in Optical Density over 24 hours, and is the value in "24hrs" - "0hrs" Column "Strain" gives the strain present in this well; this is either the Wild-Type (MG1655) or or a clone of the ASKA library containing an overexpression vector of a gene of interest (FliA+, FlhC+) Column "DC" shows whether dead cells were added or not (Yes/No) Column "IPTG" shows whether the inducer IPTG was added to this well (Yes/No) Figure S13; Biofilm assays Column "Well" gives the corresponding well number on the used microplate Column "OD" gives the Optical Density reading at timepoint 24 Column "Delta_OD" gives the change in Optical Density over 24 hours Column "Strain" gives the strain present in this well; this is either our general Wild-Type (MG1655), the Keio collection Wild-Type (BW21533) or an otherwise isogenic single gene knockout mutant of the a gene of interest (FliA, FlhC). Note that these mutants or also BW21533 E.coli. Column "DC" shows whether dead cells were added or not (Yes/No) Column "Medium" gives growth medium used (LB or M9)