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idr0151-study.txt
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105 lines (88 loc) · 9.13 KB
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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] idr0151
Study Title A timer gene network is spatially regulated by the terminal system in the Drosophila embryo
Study Type in-situ hybridization assay
Study Type Term Source REF EFO
Study Type Term Accession OBI_0001686
Study Description In insect embryos, anteroposterior patterning is coordinated by the sequential expression of the timer genes caudal, Dichaete, and odd-paired, whose expression dynamics correlate with the mode of segmentation. In Drosophila, the timer genes are expressed broadly across much of the blastoderm, which segments simultaneously, but their expression is delayed in a small tail region, just anterior to the hindgut, which segments during germband extension. Specification of the tail and the hindgut depends on the terminal gap gene tailless, but beyond this the regulation of the timer genes is poorly understood. We used a combination of multiplexed imaging, mutant analysis, and gene network modelling to resolve the regulation of the timer genes, identifying 11 new regulatory interactions and clarifying the mechanism of posterior terminal patterning. We propose that a dynamic Tailless expression gradient modulates the intrinsic dynamics of a timer gene cross-regulatory module, delineating the tail region and delaying its developmental maturation.
Study Key Words Developmental Biology Genetics Genomics Drosophila embryo patterning segmentation blastoderm terminal system gene regulatory network anteroposterior axis regulation timing
Study Organism Drosophila melanogaster
Study Organism Term Source REF NCBITaxon
Study Organism Term Accession 7227
Study Experiments Number 1
Study External URL
Study BioImage Archive Accession S-BIAD582
Study Public Release Date 2025-07-10
# Study Publication
Study PubMed ID 36524728
Study Publication Title A timer gene network is spatially regulated by the terminal system in the Drosophila embryo
Study Author List Clark E, Battistara M, Benton MA
Study PMC ID PMC10065802
Study DOI https://doi.org/10.7554/eLife.78902
# Study Contacts
Study Person Last Name Benton Clark
Study Person First Name Matthew Erik
Study Person Email matthew.benton@gmail.com ec491@cam.ac.uk
Study Person Address Developmental Biology Unit, EMBL, Germany Department of Genetics, University of Cambridge, Cambridge, United Kingdom
Study Person ORCID 0000-0001-7953-0765 0000-0002-5588-796X
Study Person Roles submitter submitter
# Study License and Data DOI
Study License CC BY 4.0
Study License URL https://creativecommons.org/licenses/by/4.0/
Study Copyright Clark et al
Study Data Publisher University of Dundee
Study Data DOI https://doi.org/10.17867/10000207
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] idr0151-clark-patterning/experimentA
Experiment Sample Type tissue
Experiment Description Fluorescent hybridisation chain reaction (HCR) RNA in situ and immunohistochemistry analysis of gene expression during embryonic patterning in wildtype and mutant Drosophila embryos.
Experiment Size 4D Images: Average Image Dimension: XYZC Total Tb: 0.335
Experiment Example Images 7a_18_wt_wg488-en546-slp594-odd647_029_mp.tif
Experiment Imaging Method confocal microscopy
Experiment Imaging Method Term Source REF Fbbi
Experiment Imaging Method Term Accession FBbi_00000251
Experiment Organism
Experiment Organism Term Source REF NCBITaxon
Experiment Organism Term Accession
Experiment Comments
# assay files
Experiment Assay File idr0151-experimentA-annotation
Experiment Assay File Format tab-delimited text
Assay Experimental Conditions Various genotypes were used. File names contain following abbreviations: genotype = 'wt' (wild-type), 'cadm' (cad[m-z+] mutant), 'cadmz' (cad[m-z-] mutant), 'cadz' (cad[m+z-] mutant), 'D' (D- mutant), 'fkh' (fkh- mutant), 'hkb' (hkb- mutant), 'opa' (opa- mutant), 'tll' (tll- mutant), 'tllopa' (tll- opa- double mutant), 'tor' (tor- mutant), or 'wg' (wg- mutant).
Assay Experimental Conditions Term Source REF
Assay Experimental Conditions Term Accession
Quality Control Description Occasional obviously atypical embryos (e.g. very small, or with abnormal patterns of mitotic division) were identified by visual inspection and discarded from the dataset.
# Protocols
Protocol Name growth protocol treatment protocol image acquisition and feature extraction protocol data analysis protocol
Protocol Type growth protocol treatment protocol image acquisition and feature extraction protocol data analysis protocol
Protocol Type Term Source REF EFO EFO
Protocol Type Term Accession EFO_0003789 EFO_0003969
Protocol Description Further detailed information on staining, mounting, imaging, etc is available with the published article (10.7554/eLife.78902) or on BioImage Archive (Accession S-BIAD582).
# 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