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KerNet, 3D fluorescence and segmentation datasets of keratin networks from MDCK, HaCaT, and RPE cells

Citation

Windoffer, Reinhard (2021), KerNet, 3D fluorescence and segmentation datasets of keratin networks from MDCK, HaCaT, and RPE cells, Dryad, Dataset, https://doi.org/10.5061/dryad.3xsj3txht

Abstract

Mechanobiology requires precise quantitative spatial information on processes taking place in specific 3D microenvironments. Connecting microscopical, molecular, biochemical and cell mechanical data with defined topologies has turned out to be extremely difficult. Establishing such structural and functional 3D maps is particular challenging for the cytoskeleton, which consists of long and interwoven filamentous polymers coordinating subcellular processes and interactions of cells with their environment. Here we present raw data and processed segmented data of fluorescence-tagged keratin intermediate filaments from MDCK, HaCaT and RPE epithelial cells. The 30 datasets contain unprocessed airyscan superresolution 3D image data and numerical network data of the 3D arrangement of the keratin intermediate filament cytoskeleton. Information is provided on network organization at the subcellular level, including mesh arrangement, density and isotropic configuration as well as details on filament morphology such as bundling, curvature and orientation. The datasets contain data in exchange format for 3d software packages. Comparison of the resulting network parameters helps to identify similarities and differences of keratin network organization in epithelial cell types. The described approach and the presented data are pivotal for generating mechanobiological models that can be experimentally tested.

Methods

Three datasets are provided:

Confocal airyscan image stacks of Madin-Darby Canine Kidney (MDCK) cells stably transfected with a plasmid encoding human full-length keratin 8 with an EYFP tag at its carboxyterminus.

Confocal airyscan image stacks of immortalized human HaCaT keratinocyte cell clone B10 expressing EYFP-tagged human keratin 5 (HK5-EYFP).

Confocal airyscan image stacks of retinal pigment epithelium that were dissected from homozygous keratin 8-YFP knock-in mice, which synthesize fluorescence-tagged keratin 8 from the modified endogenous gene locus.


The segmentation has been performed as described in the corresponding paper.

Usage Notes

We provide three rar files:

MDCK.rar
HACAT.rar
RPE.rar

Each files contains:
-  3D image data of 10 cells
-  numerical network data from 10 cells
-  a pdf file with a description of the network data
-  corresponding 3D data

Funding

Deutsche Forschungsgemeinschaft, Award: LE566/18-2

Deutsche Forschungsgemeinschaft, Award: WI173/8-2

Deutsche Forschungsgemeinschaft, Award: GRK2415/363055819

RWTH Aachen

RWTH Aachen University, Award: rwth0452