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idr0047-study.txt
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idr0047-study.txt
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# STUDY DESCRIPTION SECTION
Comment[IDR Study Accession] idr0047
Study Title A microscopy data set of discrete spatial and temporal single molecule RNA expression in single cells
Study Type fluorescence in situ hybridization
Study Type Term Source REF NCIT
Study Type Term Accession NCIT_C17563
Study Description We report a comprehensive single cell dataset of spatial distributions of nuclear and cytoplasmic mRNA as a function of time. We measure mRNA expression with single molecule RNA fluorescent in-situ hybridization microscopy in the yeast model organism Saccharomyces cerevisiae in tens of thousands of cells. The resulting dataset contains the discrete number of mRNA molecules in the nucleus and the cytoplasm for sixteen time points, two genes and two stress conditions each in biological duplicates or triplicates. We present these datasets as population means, fraction of cells above basal mRNA expression (ON-cells), the variance normalized by the expression mean (Fano factor), marginal probability of nuclear and cytoplasmic mRNA, and the joint probability of nuclear and cytoplasmic RNA expression. The reuse potential are in three areas: (1) development of discreate single cell modelling approaches, (2) building predictive models to study fundamental processes in transcription regulation, (3) development of single cell image processing approaches not possible with continuous, non-spatial datasets of low temporal resolution.
Study Organism Saccharomyces cerevisiae
Study Organism Term Source REF NCBITaxon
Study Organism Term Accession 4932
Study Experiments Number 1
Study External URL
Study BioStudies Accession S-BIAD1
Study Public Release Date 2019-01-16
# Study Publication
Study PubMed ID 31209217
Study Publication Title Multiplex RNA single molecule FISH of inducible mRNAs in single yeast cells
Study Author List Guoliang Li, Gregor Neuert
Study PMC ID PMC6572782
Study DOI https://doi.org/10.1038/s41597-019-0106-6
# Study Contacts
Study Person Last Name Neuert
Study Person First Name Gregor
Study Person Email [email protected]
Study Person Address Vanderbilt University, Nashville, TN, USA
Study Person ORCID 0000-0002-8928-6425
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 Neuert et al.
Study Data Publisher University of Dundee
Study Data DOI https://doi.org/10.17867/10000118
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] idr0047-neuert-yeastmrna/experimentA
Experiment Sample Type cell
Experiment Description We performed single molecule in-situ hybridization on yeast cells that have been exposed to osmotic stress and measured mRNA expression for two genes. The goal of this study was to generate data sets for single cell transcription modeling.
Experiment Size Average Image Dimension (XYZC): XYZCT Total Tb: 0.05546
Experiment Example Images
Experiment Imaging Method bright-field microscopy fluorescence microscopy
Experiment Imaging Method Term Source REF Fbbi
Experiment Imaging Method Term Accession FBbi_00000243 FBbi_00000246
Experiment Comments
# 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 CSM, 30C 0.2M NaCl, step TRANS: brightfield of the cells; DAPI: fluorescent stained DNA; TMR: TAMRA labeled oligo nucleotide probes that bind to an STL1 mRNA; CY5: Cy5 labeled oligo nucleotide probes that bind to an CTT1 mRNA; each image in a z-stack was 200nm apart; Nikon Ti Eclipse epifluorescent microscope equipped with perfect focus (Nikon), a 100x VC DIC lens (Nikon), fluorescent filters for DAPI, TMR and CY5 (Semrock), an X-cite 120 fluorescent light source (Excelitas), and an Orca Flash 4v2 CMOS camera (Hamamatsu); Image acquisition with Micro Manager; Image processing with Matlab using costume written scripts; TRANS and DAPI images have been used for cell segmentation; TMR and CY5 images have been used to detect RNA spots; The RNA pots are detected by a Laplacian of a Gaussian filter throughout the image stack; The RNA in the nucleus and cytoplasm was determined by multiplying the segmented nuclear and cell boundary mask with the filtered RNA images followed by counting the number of RNA in each compartment.