DOI: 10.6078/d1b13v
title: Supporting data: 3D projection electrophoresis for single-cell immunoblotting (Part 1)

description: Immunoassays and mass spectrometry are powerful single-cell protein
 analysis tools; however, interfacing and throughput bottlenecks remain.
 Here, we introduce three-dimensional single-cell immunoblots to detect
 both cytosolic and nuclear proteins. The 3D microfluidic device is a
 photoactive polyacrylamide gel with a microwell array-patterned face (x-y)
 for cell isolation and lysis. Single-cell lysate in each microwell is
 ‘electrophoretically projected’ into the 3rd dimension (z-axis),
 separated by size, and photo-captured in the gel for immunoprobing and
 confocal/light-sheet imaging. Design and analysis are informed by the
 physics of 3D diffusion. Electrophoresis throughput is &gt;2.5 cells/s
 (70X faster than published serial sampling), with 25
 immunoblots/mm2 device area (&gt;10X increase over previous
 immunoblots). The 3D microdevice design synchronizes analyses of hundreds
 of cells, compared to status quo serial analyses that impart hours-long
 delay between the first and last cell. Here, we introduce projection
 electrophoresis to augment the heavily genomic and transcriptomic
 single-cell atlases with protein-level profiling.
description: This dataset includes a mixture of different data types
 (fluorescence, confocal, and light sheet microscopy imaging as well as
 finite-element modelling) and was collected using the Methods described in
 the manuscript.  Processing used several custom MATLAB scripts.  Select
 short analysis scripts are included in the relevant data directories.
  Additional, more extensive analysis scripts to analyze various types of
 projection electrophoresis data are available in the following GitHub
 repository: https://github.com/samanthagrist/projection_ep_analysis. 
 Acquisition and processing details for each portion of the dataset are
 available in the relevant README files included in the dataset.
description: As noted in the uploaded README file in the main
 directory: <strong>Data
 Overview</strong><br> The relevant data files are
 organized into sub-directories by manuscript and SI figure, and then by
 data type and/or figure sub-panel.  Each figure directory is uploaded as a
 .zip file, and contains sub-directories.  README files describing the data
 contents are available either in the main directory or sub-directories of
 each figure directory.  In addition to these data files, quantification of
 key figures and figure panels are also available in
 ProjectionEP_ManuscriptData_SUBMIT.xlsx. Files
 included: 
 ProjectionEP_ManuscriptData_SUBMIT.xlsx — spreadsheet containing
 quantification of key figures and figure panels from the
 manuscript. Fig1_GAPDH_PTBP1.zip — archive containing
 the data relevant to Figure 1 of the manuscript
 Fig2_Purified_BSA_OVA_IgG_Lectin_Transferrin.zip — archive
 containing the data relevant to Figure 2 of the manuscript
 Fig3_Purified_BSA_OVA_IgG_Diffusion.zip — archive containing the
 data relevant to Figure 3 of the manuscript
 Fig4_Single_Cell_Assay_Development.zip — archive containing the
 data relevant to Figure 4 of the manuscript
 Fig5_Single_Cell_Analysis.zip — archive containing the data
 relevant to Figure 5 of the manuscript
 SI_Fig1_Migration_Linearity_Optimization.zip — archive
 containing the data relevant to Supplementary Figure 1 of the
 manuscript
 SI_Fig2_Diffusive_Loss_Comparison_scWB.zip — archive containing
 the data relevant to Supplementary Figure 2 of the manuscript
 SI_Fig3_Lysis_Gel_Comparison.zip — archive containing a README
 file relevant to Supplementary Figure 3 of the manuscript (data are
 included in other archives)
 SI_Fig4_Single_Cell_Analysis_Confocal.zip— archive containing
 the data relevant to Supplementary Figure 4 of the manuscript
 SI_Fig5_Spatial_Migration_Duplicate_Gel.zip— archive containing
 the data relevant to Supplementary Figure 5 of the manuscript
 SI_Fig6_Single_Cell_Migration_Comparison.zip— archive containing
 the data relevant to Supplementary Figure 6 of the manuscript
 <strong>Linked
 Data</strong><br> Large, tiled, light sheet
 microscopy images are available in separate, linked data publications due
 to file size constraints: Tiled light sheet
 microscopy image for the 'Gel 6' separation probed and imaged
 2019-10-03 ('Gel 1' in Figure 5), imaged in the GAPDH and
 Actinin protein channels (DOI: 10.6078/D1N989). Tiled
 light sheet microscopy image for the 'Gel 5' separation probed
 and imaged 2019-10-03 ('Gel 2' in Figure 5), imaged in the GAPDH
 and Actinin protein channels (DOI: 10.6078/D1811G).
 Tiled light sheet microscopy image for the 'Gel 5'
 separation probed and imaged 2019-10-03 ('Gel 2' in Figure 5),
 imaged in the GAPDH and Beta Tubulin protein channels (DOI:
 10.6078/D1HH6C, relevant only to Supplementary Figure 6).
 Please see the Related Works for links to these
 additional datasets.
 <strong>Analysis</strong><br> Select short analysis scripts are included in the relevant data directories.  Additional, more extensive analysis scripts to analyze various types of projection electrophoresis data are available in the following GitHub repository: https://github.com/samanthagrist/projection_ep_analysis