DOI: 10.5061/dryad.fbg79cp57
title: Data for: High-throughput expansion microscopy enables scalable super-resolution imaging

description: Expansion microscopy (ExM) enables nanoscale imaging using a standard
 confocal microscope through the physical, isotropic expansion of fixed
 immunolabeled specimens. ExM is widely employed to image proteins, nucleic
 acids, and lipid membranes in single cells; however, current methods limit
 the number of samples that can be processed simultaneously. We developed
 High-throughput Expansion Microscopy (HiExM), a robust platform that
 enables expansion microscopy of cells cultured in a standard 96-well
 plate. Our method enables ∼4.2x expansion of cells within individual
 wells, across multiple wells, and between plates. We also demonstrate that
 HiExM can be combined with high-throughput confocal imaging platforms to
 greatly improve the ease and scalability of image acquisition. As an
 example, we analyzed the effects of doxorubicin, a known cardiotoxic
 agent, on human cardiomyocytes (CMs) as measured by the Hoechst signal
 across the nucleus. We show a dose-dependent effect on nuclear DNA that is
 not observed in unexpanded CMs, suggesting that HiExM improves the
 detection of cellular phenotypes in response to drug treatment. Our method
 broadens the application of ExM as a tool for scalable super-resolution
 imaging in biological research applications.
description: These data were collected on an Opera Phenix high-content
 microscope using the methods described in the referenced article in
 eLife.
description: # Data for: High-throughput expansion microscopy enables scalable
 super-resolution imaging
 [https://doi.org/10.5061/dryad.fbg79cp57](https://doi.org/10.5061/dryad.fbg79cp57) ## Description of the data and file structure Folders named 'CM_Dox_X' contain images of Hoechst-stained expanded nuclei from one of the four independent biological replicates from this study. 'CM_Dox_PreEx' is the corresponding pre-expansion data, and 'CM_H2O2' is the data from the hydrogen peroxide experiment. Finally, 'Expansion_Distortion_Data' Contains all of the images that were used for non-rigid registration analysis of expansion isotropy. These data are organized into three independent experiments and further subdivided into folders containing images from single wells. These images were matched through visual assessment. All data files follow the naming convention 'rXXcXXfXX' where r and c identify the well of the 96 well plates by identifying the row (r) and column (c) of the well, and f indicates the field of view within the well. ### Files and variables #### File: CM\_Dox\_1.zip **Description:** Replicate 1 of Doxorubicin-treated cardiomyocyte study. Images are of Hoechst-stained nuclei post-expansion. #### File: CM\_Dox\_2.zip **Description:** Replicate 2 of Doxorubicin-treated cardiomyocyte study. Images are of Hoechst-stained nuclei post-expansion. #### File: CM\_Dox\_3.zip **Description:** Replicate 3 of Doxorubicin-treated cardiomyocyte study. Images are of Hoechst-stained nuclei post-expansion. #### File: CM\_DOX\_PreEx.zip **Description:** Doxorubicin-treated cardiomyocyte study. Images are of Hoechst-stained nuclei pre-expansion. #### File: CM\_Dox\_4.zip **Description:** Replicate 4 of Doxorubicin-treated cardiomyocyte study. Images are of Hoechst-stained nuclei post-expansion. #### File: CM\_H2O2.zip **Description:** Hydrogen peroxide-treated cardiomyocyte study. Images are of Hoechst-stained nuclei post-expansion. #### File: Expansion\_Distortion\_Data.zip **Description:** Expanded images of alpha-tubulin stained A549 cells with matched pre-expansion and post-expansion images for use with non-rigid registration analysis.