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idr0050-study.txt
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idr0050-study.txt
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# STUDY DESCRIPTION SECTION
Comment[IDR Study Accession] idr0050
Study Title Analysis of cyclic straining on cytoskeletal systems
Study Type immunocytochemistry
Study Type Term Source REF NCIT
Study Type Term Accession NCIT_C17731
Study Description In mammalian cells, actin, microtubules, and various types of cytoplasmic intermediate filaments respond to external stretching. Here, we investigated the underlying processes in endothelial cells plated on soft substrates from silicone elastomer. After cyclic stretch (0.13 Hz, 14% strain amplitude) for periods ranging from 5 min to 8 h, cells were fixed and double-stained for microtubules and either actin or vimentin. Cell images were analyzed by a two-step routine. In the first step, micrographs were segmented for potential fibrous structures. In the second step, the resulting binary masks were auto- or cross-correlated. Autocorrelation of segmented images provided a sensitive and objective measure of orientational and translational order of the different cytoskeletal systems. Aligning of correlograms from individual cells removed the influence of only partial alignment between cells and enabled determination of intrinsic cytoskeletal order. We found that cyclic stretching affected the actin cytoskeleton most, microtubules little, and vimentin mostly only via reorientation of the whole cell. The similarity, i.e., cross-correlation, between vimentin and microtubules was much higher than the one between actin and microtubules. Moreover, prolonged cyclic stretching slightly decoupled the cytoskeletal systems as it reduced the cross-correlations in both cases. Finally, actin and microtubules were more correlated at peripheral regions of cells whereas vimentin and microtubules correlated more in central regions.
Study Organism Homo sapiens
Study Organism Term Source REF NCBITaxon
Study Organism Term Accession 9606
Study Experiments Number 1
Study External URL
Study Public Release Date 2019-02-07
# Study Publication
Study PubMed ID 30865622
Study Publication Title Unbiased pattern analysis reveals highly diverse responses of cytoskeletal systems to cyclic straining.
Study Author List Springer R, Zielinski A, Pleschka C, Hoffmann B, Merkel R
Study PMC ID PMC6415792
Study DOI https://doi.org/10.1371/journal.pone.0210570
# Study Contacts
Study Person Last Name Merkel
Study Person First Name Rudolf
Study Person Email [email protected]
Study Person Address Institute of Complex Systems 7, Forschungszentrum Jülich GmbH, Jülich, Germany
Study Person Roles submitter
# Study License and Data DOI
Study License CC BY 4.0
Study License URL https://creativecommons.org/licenses/by/4.0/
Study Copyright Springer et al
Study Data Publisher University of Dundee
Study Data DOI https://doi.org/10.17867/10000119
Term Source Name NCBITaxon EFO CMPO FBbi NCIT
Term Source URI http://purl.obolibrary.org/obo/ http://www.ebi.ac.uk/efo/ http://www.ebi.ac.uk/cmpo/ http://purl.obolibrary.org/obo/ http://purl.obolibrary.org/obo/
# EXPERIMENT SECTION
Experiment Number 1
Comment[IDR Experiment Name] idr0050-springer-cytoskeletalsystems/experimentA
Experiment Sample Type cell
Experiment Description Characterization of cytoskeletal systems (actin, microtubules, vimentin networks) to cyclic straining using confocal laser scanning microscopy, including experiments with nocodazole to depolymerize microtubules.
Experiment Size Datasets: 4809 5D Images: Average Image Dimension (XYZCT): 1756 x 1756 x 2 x 1 x 3 Total Gb: 151.3
Experiment Imaging Method confocal microscopy phase contrast microscopy fluorescence microscopy
Experiment Imaging Method Term Source REF FBbi
Experiment Imaging Method Term Accession FBbi_00000251 FBbi_00000247 FBbi_00000246
Experiment Comments
# assay files
Experiment Assay File idr0050-experimentA-assay.txt
Experiment Assay File Format tab-delimited text
Assay Experimental Conditions
Assay Experimental Conditions Term Source REF
Assay Experimental Conditions Term Accession
Quality Control Description
# Protocols
Protocol Name growth protocol treatment protocol image acquistion and feature extraction protocol data analysis protocol
Protocol Type growth protocol treatment protocol image acquistion and feature extraction protocol data analysis protocol
Protocol Type Term Source REF
Protocol Type Term Accession
Protocol Description
# Phenotypes
Phenotype Name
Phenotype Description
Phenotype Score Type
Phenotype Term Source REF
Phenotype Term Name
Phenotype Term Accession
# Feature Level Data Files (give individual file details unless there is one file per well)
Feature Level Data File Name
Feature Level Data File Format
Feature Level Data File Description
Feature Level Data Column Name
Feature Level Data Column Description
# Processed Data Files
Processed Data File Name idr0050-experimentA-processed.txt
Processed Data File Format tab-delimited text
Processed Data File Description
Processed Data Column Name
Processed Data Column Type
Processed Data Column Annotation Level
Processed Data Column Description
Processed Data Column Link To Assay File