Is brightfield all you need for mechanism of action prediction? Image data, CellProfiler features and Grit scores
type: Dataset
description: Dataset description: The image data provided here is for U2OS cells treated with compounds belonging to ten MoA classes (MoAs that we believed would be reasonably separable and that had a sufficient number of compounds (n) associated with them in our assay). The 10 MoAs were: ATPase inhibitors (ATPase-i, n = 18); Aurora kinase inhibitors (AuroraK-i, n = 20); HDAC inhibitors (HDAC-i, n = 33); HSP inhibitors (HSP-i, n = 24); JAK inhibitors (JAK-i, n = 21); PARP inhibitors (PARP-i, n = 21); protein synthesis inhibitors (Prot.Synth.-i, n = 23); retinoid receptor agonists (Ret.Rec.Ag, n = 19); topoisomerase inhibitors (Topo.-i, n = 32); and tubulin polymerization inhibitors (Tub.Pol.-i, n = 20). The compounds were administered at a dose of 10 micromolar and exposed for 48 h, in 384 well plates. Each compound-level experiment was replicated 6 times. The compounds were distributed across 18 microplates. Images (16-bit, 2160x2160 pixels) were captured with a 20X objective at five sites/fields-of-view in each well, with five fluorescence channels for the Cell Painting fluorescence (FL) data and six evenly spaced z-planes for the brightfield (BF) data. Organization of files: 1) Raw image data: The image data for the 18 microplates ['P015076', 'P015077', 'P015080', 'P015081', 'P015082', 'P015083', 'P015084', 'P015085', 'P015090', 'P015091', 'P015092', 'P015093', 'P015094', 'P015095', 'P015096', 'P015097', 'P015098', 'P015099'] are located in the corresponding zipped folders (tar.gz). 2) Data tables: data_tables.tar.gz. This zipped folder contains the metadata pertaining to the FL (fl_data.csv) and the BF (bf_data.csv) images. Therein is given the plate, well, site (field-of-view), compound and MoA for each of the images. For FL the columns C1 to C5 give the image names for the tiff files corresponding to each of the five fluorescence channels and for BF the columns C1 to C6 correspond to the 6 z-planes. Note that the site identifiers are different for the BF and FL data, where…
creative work status: completed
  type: DefinedTerm
  in defined term set: http://publications.europa.eu/resource/authority/dataset-status
  term code: COMPLETED
creator: Philip Harrison
creator: Ankit Gupta
  type: Person
  affiliation: Science for Life Laboratory
  family name: Gupta
  given name: Ankit
creator: Jonne Rietdijk
  type: Person
  affiliation: Science for Life Laboratory
  family name: Rietdijk
  given name: Jonne
creator: Håkan Wieslander
creator: Jordi Carreras-Puigvert
creator: Polina Georgiev
  type: Person
  family name: Georgiev
  given name: Polina
creator: Carolina Wählby
  type: Person
  family name: Wählby
  given name: Carolina
creator: Ola Spjuth
  type: Person
  affiliation: Science for Life Laboratory
  family name: Spjuth
  given name: Ola
creator: Ida-Maria Sintorn
  type: Person
  family name: Sintorn
  given name: Ida-Maria
date modified: 2023-06-20
date published: 2023-06-20
keywords: Medical and Health Sciences
  type: DefinedTerm
  term code: 3
keywords: Bioinformatics (Computational Biology)
  type: DefinedTerm
  term code: 10203
keywords: Bioinformatics and computational biology not elsewhere classified
license: https://creativecommons.org/licenses/by/4.0/
publisher: Uppsala University
version: 0

PropertyValue
property ID: DOI
value: 10.17044/SCILIFELAB.21378906

Philip Harrison
type: Person
affiliation: Science for Life Laboratory
family name: Harrison
given name: Philip

Science for Life Laboratory
type: Organization

Håkan Wieslander
type: Person
family name: Wieslander
given name: Håkan

Jordi Carreras-Puigvert
type: Person
family name: Carreras-Puigvert
given name: Jordi

Uppsala University
type: Organization