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idr0053-study.txt
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idr0053-study.txt
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# STUDY DESCRIPTION SECTION
Comment[IDR Study Accession] idr0053
Study Title Virtual nanoscopy of the mouse glomerulus, mouse embryonic fibroblasts, human dendritic cells and a zebrafish embryo slice.
Study Type high resolution electron microscopy
Study Type Term Source REF
Study Type Term Accession
Study Description A key obstacle in uncovering the orchestration between molecular and cellular events is the vastly different length scales on which they occur. We describe here a methodology for ultrastructurally mapping regions of cells and tissue as large as 1 mm(2) at nanometer resolution. Our approach employs standard transmission electron microscopy, rapid automated data collection, and stitching to create large virtual slides. It greatly facilitates correlative light-electron microscopy studies to relate structure and function and provides a genuine representation of ultrastructural events. The method is scalable as illustrated by slides up to 281 gigapixels in size. Here, we applied virtual nanoscopy in a correlative light-electron microscopy study to address the role of the endothelial glycocalyx in protein leakage over the glomerular filtration barrier, in an immunogold labeling study of internalization of oncolytic reovirus in human dendritic cells, in a cryo-electron microscopy study of intact vitrified mouse embryonic cells, and in an ultrastructural mapping of a complete zebrafish embryo slice.
Study Organism Danio rerio Mus musculus Homo sapiens
Study Organism Term Source REF NCBITaxon
Study Organism Term Accession 7955 10090 9606
Study Experiments Number 1
Study External URL
Study Public Release Date
# Study Publication
Study PubMed ID 22869601
Study Publication Title Virtual nanoscopy: Generation of ultra-large high resolution electron microscopy maps
Study Author List Frank G.A. Faas, M. Cristina Avramut, Bernard M. van den Berg, A. Mieke Mommaas, Abraham J. Koster, Raimond B.G. Ravelli
Study PMC ID PMC3413355
Study DOI https://dx.doi.org/10.1083/jcb.201201140
# Study Contacts
Study Person Last Name Ravelli
Study Person First Name Raimond
Study Person Email raimond.nl@gmail.com
Study Person Address
Study Person ORCID
Study Person Roles
# Study License and Data DOI
Study License CC-BY-NC-SA
Study License URL https://creativecommons.org/licenses/by-nc-sa/3.0/
Study Copyright Faas et al.
Study Data Publisher University of Dundee
Study Data DOI https://dx.doi.org/10.1083/jcb.201201140.dv
Term Source Name NCBITaxon EFO CMPO FBbi
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/
# EXPERIMENT SECTION
Experiment Number 1
Comment[IDR Experiment Name] idr0053-faas-virtualnanoscopy/experimentA
Experiment Description Ultra-large high resolution electron microscopy maps of the mouse glomerulus, mouse embryonic fibroblasts, human dendritic cells and a zebrafish embryo slice were generated using virtual nanoscopy.
Experiment Size Total Tb:
Experiment Example Images
Experiment Imaging Method Transmission electron microscopy
Experiment Imaging Method Term Source REF Fbbi
Experiment Imaging Method Term Accession FBbi:00000258
Experiment Comments
# assay files
Experiment Assay File
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 aquistion and feature extraction protocol data analysis protocol
Protocol Type growth protocol treatment protocol image aquistion and feature extraction protocol data analysis protocol
Protocol Type Term Source REF EFO EFO
Protocol Type Term Accession
Protocol Description
# Phenotypes
Phenotype Name
Phenotype Description
Phenotype Score Type
Phenotype Term Source REF CMPO
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
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