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idr0148-study.txt
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# FILL IN AS MUCH INFORMATION AS YOU CAN. HINTS HAVE BEEN PUT IN SOME FIELDS AFTER THE HASH # SYMBOL. REPLACE THE HINT WITH TEXT WHERE APPROPRIATE.
# STUDY DESCRIPTION SECTION
# Section with generic information about the study including title, description, publication details (if applicable) and contact details
Comment[IDR Study Accession] idr0148
Study Title Ultrastructure of first trimester human fetal kidneys
Study Type electron microscopy volume map
Study Type Term Source REF EFO
Study Type Term Accession
Study Description Research on the ultrastructural development of the kidney is limited, and research on rodent kidneys prevails. Yet, large differences between rodent and human nephrogenesis exist and therefore translation between species is not desirable. At the same time, there is an increasing demand for human research, in addition to assessing the potential of novel therapies such as renal organoids. We therefore generated an interactive atlas of large transmission electron microscopy tile scans of first trimester human kidneys, specifically Carnegie stage 20 until post-conceptional week 12. Analysis identified key ultrastructural features of proximal and distal progenitor cells such as cell shape, microvilli and luminal budding in the renal vesicle. Regarding glomerular development, we identified a new W-shaped body stage and three distinct sub-stages of the well-known capillary loop stage. Chromatin organization, nuclear shape and location were used to describe tubule cell identity and maturity, indicating a specific order of tubular maturation. The greatest congruence with adult tissue was seen in proximal tubules and the least in distal tubules. Finally, cytoplasmic glycogen depositions in collecting duct cells, which are absent in adult tissue, were found to be an early feature distinguishing distal tubules from collecting ducts as well as differentiating cortical from medullary collecting ducts. The findings of this research provide new fundamental insights for researchers who aim to understand and recreate kidney development.
Study Key Words Nephrogenesis Human kidney development Transmission electron microscopy FIB-SEM Capillary loop stage Ultrastructure
Study Organism Homo sapiens
Study Organism Term Source REF NCBITaxon
Study Organism Term Accession 9606
Study Experiments Number 1
Study External URL
Study BioImage Archive Accession
Study Public Release Date 2023-04-05
# Study Publication
Study PubMed ID
Study Publication Title Structural development of the human fetal kidney: new stages and cellular dynamics in nephrogenesis
Study Author List Schumacher A, Nguyen TQ, Broekhuizen R, van Griensven M, LaPointe V
Study PMC ID
Study DOI
# Study Contacts
Study Person Last Name Schumacher
Study Person First Name Anika
Study Person Email [email protected]
Study Person Address Universiteitssingel 40, Maastricht, The Netherlands
Study Person ORCID 0000-0001-7790-2756
Study Person Roles submitter and first author
# Study License and Data DOI
Study License CC BY 4.0
Study License URL https://creativecommons.org/licenses/by/4.0/
Study Copyright Schumacher et al
Study Data Publisher University of Dundee
Study Data DOI https://doi.org/10.17867/10000192
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 Section containing all information relative to each experiment in the study including materials used, protocols names and description, phenotype names and description. For multiple experiments this section should be repeated. Copy and paste the whole section below and fill out for the next experiment
Experiment Number 1
Comment[IDR Experiment Name] idr0148-schumacher-kidneytem/experimentA
Experiment Sample Type tissue
Experiment Description Development of human fetal kidneys of first trimester were assessed using large transmission electron microscopy tilescans.
Experiment Size 5D Images: Average Image Dimension (XYZCT): Total Tb:
Experiment Example Images
Experiment Imaging Method transmission electron microscopy (TEM) bright-field microscopy
Experiment Imaging Method Term Source REF Fbbi Fbbi
Experiment Imaging Method Term Accession FBbi_00000258 FBbi_00000243
Experiment Organism
Experiment Organism Term Source REF NCBITaxon
Experiment Organism Term Accession
Experiment Comments
# assay files
Experiment Assay File idr0148-experimentA-annotation
Experiment Assay File Format tab-delimited text
Assay Experimental Conditions
Assay Experimental Conditions Term Source REF
Assay Experimental Conditions Term Accession
Quality Control Description Health of tissues was assessed using histological slides by two independent nephropathologists at the beginning of the study.
# Protocols
Protocol Name Light microscopy of stained paraffin sections
Protocol Type image acquisition
Protocol Type Term Source REF EFO EFO
Protocol Type Term Accession
Protocol Description Sections of 3 μm thickness were cut from the paraffin embedded kidneys and were stained with Periodic acid-Schiff (PAS).
The sections were imaged using a 10× air objective on an automated Nikon Eclipse Ti-E.
The sections were used to assess te health of all tissues by two independent nephropathologists at the beginning of the study.
Protocol Name Light microscopy of stained semithin sections
Protocol Type image acquisition
Protocol Type Term Source REF EFO EFO
Protocol Type Term Accession
Protocol Description Sections of 1 μm thickness (semithin) were cut from the Epon embedded kidneys and stained with toluidine blue.
The sections were imaged using a 20× air objective on an automated Nikon Eclipse Ti-E.
In these images the regions of interest (ROIs) were determined for transmission electron microscopy imaging and analysis.
Protocol Name TEM image acquisition and processing
Protocol Type image acquisition and feature extraction protocol
Protocol Type Term Source REF EFO EFO
Protocol Type Term Accession
Protocol Description The region of interest (ROI) was determined in toluidine blue stained 1 μm sections of the Epon embedded kidneys.
Ultrathin sections of 60 nm were then cut of the determined ROI on a Leica UC7 ultramicrotome and stained with 2% uranyl acetate and Reynold’s lead citrate.
The ultrathin sections were observed on a Tecnai T12 electron microscope equipped with an Eagle 4k × 4k CCD camera (Thermo Fisher Scientific).
To target the ROI, full-section scans were made using the EPU software (1.6.0.1340REL, FEI).
Subsequently, the ROI (determined earlier in the toluidine blue stained sections) was imaged in tiles at 2900× magnification using the EM Mesh software (version 6).
Data were stitched, uploaded and annotated for the analysis using Omero and PathViewer.
# 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