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idr0040-study.txt
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idr0040-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] idr0040
Study Title Timing of gene expression in a cell-fate decision system
Study Type time-lapse imaging
Study Type Term Source REF OMIT
Study Type Term Accession OMIT_0027490
Study Description During development, morphogens provide extracellular cues allowing cells to select a specific fate by inducing complex transcriptional programs. The mating pathway in budding yeast offers simplified settings to understand this process. Pheromone secreted by the mating partner triggers the activity of a MAPK pathway, which results in the expression of hundreds of genes. Using a dynamic expression reporter, we quantified the kinetics of gene expression in single cells upon exogenous pheromone stimulation and in the physiological context of mating. In both conditions, we observed striking differences in the timing of induction of mating-responsive promoters. Biochemical analyses and generation of synthetic promoter variants demonstrated how the interplay between transcription factor binding and nucleosomes contribute to determine the kinetics of transcription in a simplified cell-fate decision system.
Study Organism Saccharomyces cerevisiae
Study Organism Term Source REF NCBITaxon
Study Organism Term Accession NCBITaxon_4932
Study Experiments Number 1
Study External URL
Study Public Release Date 2018-04-12
# Study Publication
Study PubMed ID 29695607
Study Publication Title Timing of gene expression in a cell-fate decision system.
Study Author List Aymoz D, Solé C, Pierre JJ, Schmitt M, de Nadal E, Posas F, Pelet S
Study PMC ID PMC5916086
Study DOI https://doi.org/10.15252/msb.20178024
# Study Contacts
Study Person Last Name Pelet
Study Person First Name Serge
Study Person Email [email protected]
Study Person Address Département de Microbiologie Fondamentale - Bâtiment Biophore - 1015 Lausanne
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 Pelet et al
Study Data Publisher University of Dundee
Study Data DOI https://doi.org/10.17867/10000114
Term Source Name NCBITaxon EFO CMPO FBbi OMIT
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] idr0040-aymoz-singlecell/experimentA
Experiment Data Publisher
Experiment Data DOI
Experiment Sample Type cell
Experiment Description Time-lapse with addition of 1uM alpha-factor at time 0
Experiment Size 5D Images: 1 Tb
Experiment Example Images https://idr.openmicroscopy.org/webclient/?show=image-3491616 https://idr.openmicroscopy.org/webclient/img_detail/3491616/
Experiment Imaging Method fluorescence microscopy
Experiment Imaging Method Term Source REF Fbbi
Experiment Imaging Method Term Accession FBbi_00000246
Experiment Comments
# assay files
Experiment Assay File idr0040-experimentA-assays.txt
Experiment Assay File Format comma-delimited text file
Assay Experimental Conditions
Assay Experimental Conditions Term Source REF
Assay Experimental Conditions Term Accession
Quality Control Description
# Protocols
Protocol Name "Overnight + 4h" "Pheromone treatment" "Time-lapse induction" "YeastQuant analysis"
Protocol Type "Overnight + 4h" "Pheromone treatment" "Time-lapse induction" "YeastQuant analysis"
Protocol Type Term Source REF
Protocol Type Term Accession
Protocol Description "The cells were grown overnight in selective synthetic medium to saturation (YNB:CYN3801, CSM:DCS0031, ForMedium). They were diluted to an OD600 of 0.05 in the morning and grown for 4 hours before starting the experiment." "All the time-lapse experiments were performed in well slides, for which selected wells of 96-well plates (MGB096-1-2LG, Matrical Bioscience) were coated with filtered solution of Concanavalin A in H2O (0.5 mg/ml, C2010-250MG, Sigma- Aldrich) for 30 minutes, rinsed with H2O and dried for at least ten hours. Before the experiments, the cells were diluted to an OD600 of 0.04, briefly sonicated, and 200μL of cell suspension were added to a well. Imaging was started 30 minutes later, so as to let the cells settle to the bottom to the well. To stimulate the cells, 100 μL of a 3 μM solution of synthetic exogenous α-factor (gift from M. Peter’s lab.) was added in the well before the 4th timepoint to reach a final 1 μM concentration of pheromone." "Images were acquired on a fully automated inverted epi-fluorescence microscope (Ti-Eclipse, Nikon) controlled by Micro-Manager (Edelstein et al, 2010) and placed in an incubation chamber set at 30°C, with a 40X oil objective and appropriate excitation and emission filters. The excitation was provided by a solid-state light source (SpectraX, Lumencor). The images were recorded with a sCMOS camera (Flash4.0, Hamamatsu). A motorized XY-stage allowed recording multiple fields of view at every time point, typically 5 positions per well. CFP (50ms), RFP (300ms) and YFP (300ms) and 2 bright-field (10ms) images were recorded at time intervals of 5 minutes." "Time-lapse movies were analyzed with the YeastQuant platform (Pelet et al, 2012). Briefly, the nuclei of the cells were segmented by thresholding of the CFP images. The contour of the cell around each nucleus was detected using two bright-field images. The cytoplasm object was obtained by removing the nucleus object expanded by two pixels from the cell object. "
# 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
Processed Data File Format
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