Data for "Signaling through polymerization and degradation: Analysis and simulations of T cell activation mediated by Bcl10" By Leonard Campanello, Maria Traver, Hari Shroff, Brian Schaefer, and Wolfgang Losert This repository contains 4 directories: 1. Raw Image Data 2. Processed Image Data 3. Analyzed Image Data 4. Simulations Data 1. Raw Image Data: - Contains the raw iSIM image data described in the manuscript - The directory called "20 min" contains the images taken 20 min post activation - The directory called "40 min" contains the images taken 40 min post activation 2. Processed Image Data - Contains processed images for each cell in each of the iSIM images in "Raw Image Data" - The description of each file contained is as follows: a. "RoughMask.tif" is the manually annotated mask that should be applied to the raw image b. "Channel1_binary.tif" is the segmented objects obtained from processing channel 1 of the raw data within "RoughMask.tif" c. "Channel2_binary.tif" is the segmented objects obtained from processing channel 2 of the raw data within "RoughMask.tif" d. "CellMask.tif" is the cell boundary that was calculated from processing channels 1 and 2 of the raw data within "RoughMask.tif" e. "Channel2_skeleton.tif" is the medial-axis skeletons of the binary objects in "Channel2_binary.tif" 3. Analyzed Imaged Data - Contains results from the analysis of the data in "Processed Image Data" - The description of each file contained is as follows: a. "FilamentLengths.csv" are the lengths in microns of each Bcl10 structure in the corresponding processed image as per the skeleton in "Channel2_skeleton.tif". Values of -1 are puncta. b. "ContactEdgeDistances.csv" and "ContactEdgeDistanceWeights.csv": Each row represents a SINGLE Bcl10-autophagosome contact (i.e., the overlay between "Channel1_binary.tif" and "Channel2_binary.tif"). The overlapping voxels may span multiple edge-distance regions along the Bcl10 structure; thus, each edge-distance value and the corresponding weight of that value (i.e. the relative number of voxels in the region) were recorded. 4. Simulations Data - Contains the results from the simulations described in the manuscript - The folders with prefix "20_" contain the results for each of the 1000 simulations performed with the parameters described in the folder name - The folder name breakdown is as follows: a. attach_pBefore= pAttach in the manuscript b. carma1_pActivate= pActivate in the manuscript c. Degrade Meth 0 is when there is no degradation (used in Figure 4 of the manuscript) d. Degrade Meth 2 is when there is degradation (used in Figure 5 of the manuscript) In such cases, pDegrade= pDegrade in the manuscript - For example, folder "20_attach_pBefore=0.001_carma1_pActivate=0.010_Degrade Meth 2_Degrade pDegrade=0.01" is pAttach = 0.001 pActivate = 0.01 pDegrade = 0.01 - Within each folder are files with prefixes "DataMovie2_" which contain the raw simulations data - The file name breakdown is as follows: a. bclInitLevel= is the number of Bcl10 monomers initialized in the simulation b. carma1InitLevel= the number of nucleation sites initialized in the simulation c. degradeMethod= is the degradation method (either 0 for no degradation, or 2 for with degradation) d. _vN where N = the Nth iteration of the simulations with the same initial condition - For example, file "DataMovie2_bclInitLevel=9085_carmaInitLevel=22_degradeMethod=2_v5" is initial number of Bcl10 monomers = 9085 number of nucleation sites = 22 with degradation the 5th repeat of the simulation with those initial conditions