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idr0133-study.txt
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idr0133-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] idr0133
Study Title Reference compounds for characterizing cellular injury in high-content cellular morphology assays
Study Type high content screen
Study Type Term Source REF EFO
Study Type Term Accession EFO_0007550
Study Description Robust, generalizable approaches to efficiently identify compounds with undesirable mechanisms of action in complex cellular assays remain elusive. Such a process would be useful for hit triage during high-throughput screening and, ultimately, predictive toxicology during drug development. Here, we report on the generation of Cell Painting and cellular health profiles for 218 prototypical cytotoxic and nuisance compounds in U-2 OS cells in a concentration-response format. Compounds causing cellular damage such as cytoskeletal poisons, genotoxins, nonspecific electrophiles, and redox-active compounds produced bioactive Cell Painting morphologies. Further, we show that lower-quality lysine acetyltransferase inhibitors and nonspecific electrophiles can be distinguished from more selective counter-parts. We propose that the purposeful inclusion of cytotoxic and nuisance reference compounds such as those profiled in this Resource will help with assay optimization and compound prioritization in complex cellular assays like Cell Painting.
Study Key Words cell painting chemical biology cytotoxicity drug discovery high-content screening nuisance compounds
Study Organism Homo sapiens
Study Organism Term Source REF NCBITaxon
Study Organism Term Accession 9606
Study Screens Number 1
Study External URL
Study BioImage Archive Accession
Study Public Release Date 2022-07-05
# Study Publication
Study PubMed ID 36914634
Study Publication Title Reference compounds for characterizing cellular injury in high-content cellular morphology assays
Study Author List Dahlin JL, Hua BK, Zucconi BE, Nelson Jr. SD, Singh S, Carpenter AE, Shrimp JH, Lima-Fernandes E, Wawer MJ, Chung LPW, Agrawal A, O’Reilly M, Barsyte-Lovejoy D, Szewczyk M, Li F, Lak P, Cuellar M, Cole PA, Meier JL, Thomas T, Baell JB, Brown PJ, Walters MA, Clemons PA, Schreiber SL, Wagner BK
Study PMC ID PMC10011410
Study DOI https://doi.org/10.1038/s41467-023-36829-x
# Study Contacts
Study Person Last Name Dahlin
Study Person First Name Jayme
Study Person Email [email protected]
Study Person Address NCATS, 9800 Medical Center Drive, Rockville, Maryland, 20850, USA
Study Person ORCID 0000-0003-4151-9944
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 Dahlin & Hua et al
Study Data Publisher University of Dundee
Study Data DOI
Term Source Name NCBITaxon EFO CMPO Fbbi
Term Source File http://purl.obolibrary.org/obo/ http://www.ebi.ac.uk/efo/ http://www.ebi.ac.uk/cmpo/ http://purl.obolibrary.org/obo/
# SCREEN SECTION
# Screen Section containing all information relative to each screen in the study including materials used, protocols names and description, phenotype names and description.
# For multiple screens this section should be repeated. Copy and paste the whole section below and fill out for the next screen.
Screen Number 1
Comment[IDR Screen Name] idr0133-dahlin-cellpainting/screenA
Screen Sample Type cell
Screen Description We screened 218 prototypical cytotoxic and nuisance compounds in U-2 OS cells in concentration-response format using the Cell Painting assay. From a previous Cell Painting experiment, an additional 283 compounds with either high or no correlation to a gross cell injury morphology were re-tested in single-concentration format.
Screen Size Plates: 5D Images: Planes: 1 Average Image Dimension (XYZCT): Total Tb:
Screen Example Images
Screen Imaging Method fluorescence microscopy
Screen Imaging Method Term Source REF Fbbi
Screen Imaging Method Term Accession FBbi_00000246
Screen Technology Type compound screen
Screen Technology Type Term Source REF EFO
Screen Technology Type Term Accession EFO_0007553
Screen Type primary screen
Screen Type Term Source REF EFO
Screen Type Term Accession EFO_0007556
Screen Comments Missing wells are compounds that failed analytical quality control (UPLC-MS) or compounds from other studies.
# Library section. The library file should be supplied separately and it should contain the reagents description including, at the absolute minimum: reagent ID, sequences and position in the layout (= plate + position in the plate)
Library File Name idr0133-screenA-annotation.csv
Library File Format tab-delimited text
Library Type compound library
Library Type Term Source REF EFO
Library Type Term Accession EFO_0007569
Library Manufacturer Library compounds were obtained from a variety of sources (Aldrich Market Select, Cayman Chemicals, AbbVie, in-house syntheses, etc.)
Library Version 1
Library Experimental Conditions
Library Experimental Conditions Term Source REF EFO
Library Experimental Conditions Term Accession
Quality Control Description UPLC-MS and manufacturer certificate of analysis inspection
# Protocols
Protocol Name growth protocol treatment protocol HCS library protocol HCS image acquisition and feature extraction protocol HCS data analysis protocol
Protocol Type growth protocol treatment protocol HCS library protocol HCS image acquisition and feature extraction protocol HCS data analysis protocol
Protocol Type Term Source REF EFO EFO EFO EFO EFO
Protocol Type Term Accession EFO_0003789 EFO_0003969 EFO_0007571 EFO_0007572 EFO_0007573
Protocol Description Please see study publication for details regarding cell culture conditions. Please see study publication for details regarding cell treatment conditions. Prototypical cytotoxic and nuisance compounds were chosen based on literature review, institutional experience, and author experience. Please see study publication for details regarding labeling, imaging hardware and software, and feature extraction methods. Please see study publication for details regarding analysis of the images and features.
# Phenotypes
Phenotype Name
Phenotype Description
Phenotype Score Type
Phenotype Term Source REF CMPO
Phenotype Term Name
Phenotype Term Accession
# Raw Data Files
Raw Image Data Format TIFF
Raw Image Organization 84 x 384 well plates, 9 fields per well. Each field was imaged in five channels (detection wavelengths). Each channel is stored as a separate, grayscale image file in 16-bit TIFF format.
# Feature Level Data Files
Feature Level Data File Name
Feature Level Data File Description
Feature Level Data File Format
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 Library File