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idr0037-study.txt
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"# Section with generic information about the study including title, description, publication details (if applicable) and contact details"
# Study
Comment[IDR Study Accession] idr0037
Study Title Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors
Study Type high content screen
Study Type Term Source REF EFO
Study Type Term Accession EFO_0007550
Study Description Large cohorts of human induced pluripotent stem cells (iPSCs) from healthy donors are a potentially powerful tool for investigating the relationship between genetic variants and cellular behavior. Here, we integrate high content imaging of cell shape, proliferation, and other phenotypes with gene expression and DNA sequence datasets from over 100 human iPSC lines. By applying a dimensionality reduction approach, Probabilistic Estimation of Expression Residuals (PEER), we extracted factors that captured the effects of intrinsic (genetic concordance between different cell lines from the same donor) and extrinsic (cell responses to different fibronectin concentrations) conditions. We identify genes that correlate in expression with intrinsic and extrinsic PEER factors and associate outlier cell behavior with genes containing rare deleterious non-synonymous SNVs. Our study, thus, establishes a strategy for examining the genetic basis of inter-individual variability in cell behavior.
Study Organism Homo sapiens
Study Organism Term Source REF NCBITaxon
Study Organism Term Accession NCBITaxon_9606
Study Screens Number 1
Study External URL http://www.hipsci.org/
Study Public Release Date
# Study Publication
Study PubMed ID 30784590
Study Publication Title Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors
Study Author List Alessandra Vigilante, Anna Laddach, Nathalie Moens, Ruta Meleckyte, Andreas Leha, Arsham Ghahramani, Oliver J. Culley, Annie Kathuria, Chloe Hurling, Alice Vickers, Erika Wiseman, Mukul Tewary, Peter W. Zandstra, HipSci Consortium, Richard Durbin, Franca Fraternali, Oliver Stegle, Ewan Birney, Nicholas M. Luscombe, Davide Danovi, Fiona M. Watt
Study PMC ID
Study DOI https://doi.org/10.1016/j.celrep.2019.01.094
# Study License and Data DOI
Study License CC-BY 4.0
Study License URL https://creativecommons.org/licenses/by/4.0/
Study Copyright Vigilante et al
Study Data Publisher University of Dundee
Study Data DOI https://doi.org/10.17867/10000120
# Study Contacts
Study Person Last Name Danovi
Study Person First Name Davide
Study Person Email [email protected]
Study Person Address Centre for Stem Cells & Regenerative Medicine, King's College London, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, United Kingdom
Study Person Roles submitter
Term Source Name NCBITaxon EFO CMPO FBbi PATO CL CHEBI
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/ http://purl.obolibrary.org/obo/ http://purl.obolibrary.org/obo/
"# Section containing all information relative to each screen in the study including materials used, protocols names and description, phenotype names and description. For multiple assays this section should be repeated."
# Screen; this section should be repeated if a study contains multiple screens
Screen Number 1
Comment[IDR Screen Name] idr0037-vigilante-hipsci/screenA
Screen Description Cellular phenotyping of 115 human induced pluripotent stem cell lines from 67 donors within the framework of the HipSci project. Cells are plated sparsely, 3000 per 96 well for 24 hours on wells coated with three diverse concentrations of Fibronectin. This screen is an extension of a previous screen and includes all data from idr0034.
Screen Size Plates: 69 5D Images: Planes: 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 cell line screen
Screen Technology Term Source REF
Screen Technology Term Accession
Screen Type primary screen
Screen Type Term Source REF EFO
Screen Type Term Accession EFO_0007556
Screen Comments
"# 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 idr0037-screenA-library.txt
Library File Format tab-delimited text
Library Type cell line library
Library Type Term Source REF
Library Type Term Accession
Library Manufacturer
Library Version
Library Experimental Conditions
Library Experimental Conditions Term Source REF
Library Experimental Conditions Term Accession
Quality Control Description
# Protocols
Protocol Name growth protocol HCS image acquistion and feature extraction protocol HCS data analysis protocol
Protocol Type growth protocol HCS image acquistion and feature extraction protocol HCS data analysis protocol
Protocol Type Term Source REF EFO EFO EFO
Protocol Type Term Accession EFO_0003789 EFO_0007572 EFO_0007573
Protocol Description
# Phenotypes
Phenotype Name
Phenotype Description
Phenotype Score Type
Phenotype Term Source REF
Phenotype Term Name
Phenotype Term Accession
# Raw Data Files
Raw Image Data Format Operetta
Raw Image Organization There are 69 x 96 wells plates with 9 fields per well and 4 channels. 29 of the plates are also in idr0034 but with images from different wells shown in the plates that are in common.
# Feature Level Data Files (give individual file details unless there is one file per well)
Feature Level Data File Name
Feature Level Data File Description
Feature Level Data File Format
Feature Level Data Column Name
Feature Level Data Column Type
Feature Level Data Column Description
# Processed Data Files
Processed Data File Name idr0037-screenA-processed.txt
Processed Data File Format tab-delimited text
Processed Data File Description Provides links to files containing well and cell level measurements, and to documents containing analysis summaries.
Processed Data Column Name Characteristics [Cell Line] Results Measurements Results Summary
Processed Data Column Type other other other
Processed Data Column Annotation Level cell line cell line
Processed Data Column Description The name of the cell line the results are related to Links to FTP directories containing measurements derived for each cell. Links to FTP directories containing summaries of analyses.
Processed Data Column Link To Library File Characteristics [Cell Line]