Data for: High-throughput expansion microscopy enables scalable super-resolution imaging
Data files
Nov 04, 2024 version files 47.35 GB
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CM_Dox_1.zip
10.05 GB
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CM_Dox_2.zip
8.13 GB
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CM_Dox_3.zip
10.09 GB
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CM_Dox_4.zip
8.73 GB
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CM_DOX_PreEx.zip
114.58 MB
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CM_H2O2.zip
9.38 GB
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Expansion_Distortion_Data.zip
851.27 MB
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README.md
2.18 KB
Abstract
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.
README: Data for: High-throughput expansion microscopy enables scalable super-resolution imaging
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.
Methods
These data were collected on an Opera Phenix high-content microscope using the methods described in the referenced article in eLife.