DOI: 10.5061/dryad.70rxwdcc1
title: Ballistic Microscopy (BaM) data repository

description: Light and electron microscopy utilizes interactions of either photons or
 electrons with matter to create images from cellular to atomic scale.
 However, these methods are limited in de novo discovery and spatial
 mapping of unknown biomolecules. Label-free methods, such as mass
 spectrometry or sequencing, lack live-cell and subcellular context. Here,
 we introduce a new approach, Ballistic Microscopy (BaM), to image cells
 with physical nanoparticles. We bombard living cells with millions of
 nanoparticles traveling at ∼1000 m/s. Each particle passes through cells,
 piercing and capturing attoliters of cytoplasm on a hydrogel substrate
 while preserving spatial information (SPLAT-MAP). This “physical image” of
 a live cell captures a molecular fingerprint of a cell on a hydrogel film
 that can be processed post-capture via multiple techniques such as TEM,
 Cryo-EM, mass spectrometry, confocal imaging, and DNA amplification. Using
 BaM, we discover a previously unknown composition of CLIP170 and Tau3R
 condensates in HEK cells, uncovering Keratin-18 as a structural element.
 BaM establishes a new paradigm of “physical imaging” with a modular
 readout platform for spatially resolved live sampling across cells,
 tissues, and organisms.
description: # Ballistic Microscopy (BaM) data repository Dataset DOI:
 [10.5061/dryad.70rxwdcc1](https://doi.org/10.5061/dryad.70rxwdcc1) ##
 Description of the data and file structure The contents of this dataset
 were used in the associated preprint "Ballistic Microscopy
 (BaM)." It includes multiple data, including confocal fluorescence
 microscopy, transmission electron microscopy (TEM), cryo-electron
 microscopy (cryo-EM), high-speed imaging, mass spectrometry data from
 CLIP-170 condensates, and protein gel images. This dataset contains
 several types of data used in the manuscript. File names are organized and
 labeled according to main figures, supplementary figures, videos, and
 supplementary tables. .xlsx files can be opened using Microsoft Excel;
 .mrc and .tif files can be opened using ImageJ/Fiji; .cys files can be
 opened using Cytoscape; and .stl files can be opened using PrusaSlicer. ##
 **01 Table S2. List of proteins in CLIP170 condensates.pdf** *
 01_Table_S2._List_of_proteins_in_CLIP170_condensates.pdf * This file
 contains the list of proteins identified in CLIP-170 condensates, derived
 from pooled BaM mass spectrometry experiments. Proteins are listed with
 associated annotations used in the manuscript. ## **02 Table S3 Materials
 reagents and antibodies.xlsx** *
 Table_S3_Materials__reagents_and_antibodies.xlsx * This Excel file
 provides a comprehensive list of materials, reagents, and antibodies used
 in this study, including sources and identifiers, following standard
 reporting guidelines. * Variables (Excel/ Spreadsheet Data): * Resource or
 Reagent - Name of the material, reagent, or antibody. * Source - Supplier
 or manufacturer. * Identifier - Catalog number, or other unique
 identifier. * All variables are categorical text fields and do not have
 physical units. ## **Fig. 4G and SV3a Cryo-EM tilt series.mrc** *
 Fig._4G_and_SV3a_Cryo-EM_tilt_series.mrc This file contains the raw
 cryo-electron microscopy tilt series used for structural analysis and
 visualization associated with Figure 4G and Supplementary Video 3a. ##
 **Fig. 5F GFP-CLIP170 BaM mass spectrometry.cys** *
 Fig._5F_GFP-CLIP170_BaM_mass_spectrometry.cys * Cytoscape network file
 representing the protein interaction network identified from BaM mass
 spectrometry of GFP-CLIP-170 condensates. ## **Fig. 5G GFP control BaM
 mass spectrometry.cys** * Fig._5G_GFP_control_BaM_mass_spectrometry.cys *
 Cytoscape network file representing the protein interaction network
 obtained from BaM mass spectrometry of GFP control samples. ## **Fig. 5J
 Fig. S8H SV4 CLIP 170 Keratin 14 Z stack panel A.tif** ## **Fig. S8I SV4
 CLIP 170 Keratin 14 Z stack panel B.tif** *
 Fig._5J_Fig.S8H_SV4_CLIP_170_Keratin_14_Z_stack_panel_A.tif *
 Fig.S8I_SV4_CLIP_170_Keratin_14_Z_stack_panel_B.tif * Fluorescence
 microscopy Z-stack images showing CLIP170 and Keratin-14 localization and
 organization, corresponding to main and supplementary figures and videos.
 ## **Fig. 5L Fig. S8J SV5 Tau 3R Keratin 18 Z stack.tif** *
 Fig._5L_Fig.S8J_SV5_Tau_3R_Keratin_18_Z_stack.tif * Fluorescence
 microscopy Z-stack image illustrating Tau 3R and Keratin-18 organization
 in condensates and aggregates. ## **Fig. S4D TEM panel a.tif** ## **Fig.
 S4D TEM panel b.tif** Transmission electron microscopy images associated
 with Supplementary Figure S4D. ## **Fig. S4E TEM panel a-h.tif** *
 Fig._S4D_TEM_panel_a.tif * Fig._S4D_TEM_panel_b.tif *
 Fig._S4E_TEM_panel_a.tif * Fig._S4E_TEM_panel_b.tif *
 Fig._S4E_TEM_panel_c.tif * Fig._S4E_TEM_panel_d.tif *
 Fig._S4E_TEM_panel_e.tif * Fig._S4E_TEM_panel_f.tif *
 Fig._S4E_TEM_panel_g.tif * Fig._S4E_TEM_panel_h.tif Transmission electron
 microscopy panels corresponding to Supplementary Figure S4E, showing
 ultrastructural features observed in BaM-related experiments. ## **Fig.
 S6C protein gel.tif** * Fig._S6C_protein_gel.tif * Protein gel image used
 to validate protein expression and purification steps described in the
 manuscript. ## **Fig. S5 Cryo-EM panel a-c.tif** ## **Fig. S5 Cryo-EM BaM
 panel d-l.tif** * Fig.S5_Cryo-EM_BaM_panel_d.tif -
 Fig.S5_Cryo-EM_BaM_panel_e.tif * Fig.S5_Cryo-EM_BaM_panel_f.tif -
 Fig.S5_Cryo-EM_BaM_panel_g.tif * Fig.S5_Cryo-EM_BaM_panel_h.tif -
 Fig.S5_Cryo-EM_BaM_panel_i.tif * Fig.S5_Cryo-EM_BaM_panel_j.tif -
 Fig.S5_Cryo-EM_BaM_panel_k.tif * Fig.S5_Cryo-EM_BaM_panel_l.tif -
 Fig.S5_Cryo-EM_panel_a.tif * Fig.S5_Cryo-EM_panel_b.tif -
 Fig.S5_Cryo-EM_panel_c.tif Cryo-electron microscopy images associated with
 Supplementary Figure S5, including conventional cryo-EM and BaM-derived
 samples. ## **File to 3D print an EM grid holder that fits in a PCR
 tube.zip** *
 File_to_3D_print_an_EM_grid_holder_that_fits_in_a_PCR_tube.zip * This
 archive contains STL files required to 3D-print a custom EM grid holder
 designed to fit inside a PCR tube, as described in the methods. ##
 Code/Software No new code was generated in this study.