Human MCF7 cells – compound-profiling experiment (BBBC021v1)
The Broad Institute

folder BBBC021 (58 files)
fileBBBC021_v1_compound.csv 8.18kB
fileBBBC021_v1_image.csv 3.97MB 839.44MB 851.40MB 841.37MB 854.60MB 861.58MB 874.85MB 813.32MB 812.95MB 817.95MB 819.82MB 744.17MB 800.66MB 871.46MB 857.91MB 866.10MB 872.82MB 872.58MB 879.70MB 821.23MB 900.82MB 842.01MB 887.88MB 869.27MB 859.01MB 855.93MB 871.72MB 842.79MB 852.25MB 863.88MB 873.15MB 820.70MB 858.47MB 800.43MB 805.25MB 821.45MB 736.92MB 848.89MB 807.29MB 878.01MB 871.25MB 869.46MB 784.99MB 821.32MB 765.06MB 781.85MB 770.98MB 781.36MB
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Type: Dataset
Tags: Medical, Biology

title= {Human MCF7 cells – compound-profiling experiment (BBBC021v1)},
keywords= {Medical, Biology},
author= {The Broad Institute},
abstract= {![](


### Description of the biological application
Phenotypic profiling attempts to summarize multiparametric, feature-based analysis of cellular phenotypes of each sample so that similarities between profiles reflect similarities between samples. Profiling is well established for biological readouts such as transcript expression and proteomics. Image-based profiling, however, is still an emerging technology.

This image set provides a basis for testing image-based profiling methods wrt. to their ability to predict the mechanisms of action of a compendium of drugs. The image set was collected using a typical set of morphological labels and uses a physiologically relevant p53-wildtype breast-cancer model system (MCF-7) and a mechanistically distinct set of targeted and cancer-relevant cytotoxic compounds that induces a broad range of gross and subtle phenotypes.

### Images
The images are of MCF-7 breast cancer cells treated for 24 h with a collection of 113 small molecules at eight concentrations. The cells were fixed, labeled for DNA, F-actin, and Β-tubulin, and imaged by fluorescent microscopy as described [Caie et al. Molecular Cancer Therapeutics, 2010].

There are 39,600 image files (13,200 fields of view imaged in three channels) in TIFF format. We provide the images in 55 ZIP archives, one for each microtiter plate.

### Metadata
The file BBBC021_v1_image.csv contains the metadata, with the following fields:


### Ground truth B
A subset of the compound-concentrations have been identified as clearly having one of 12 different primary mechanims of action. mechanistic classes were selected so as to represent a wide cross-section of cellular morphological phenotypes. The differences between phenotypes were in some cases very subtle: we were only able to identify 6 of the 12 mechanisms visually; the remainder were defined based on the literature.

The file BBBC021_v1_moa.csv contains the mechanisms of action of 103 compound-concentrations (38 compounds at 1–7 concentrations each). The fields are:


### Recommended citation

"We used image set BBBC021v1 [Caie et al., Molecular Cancer Therapeutics, 2010], available from the Broad Bioimage Benchmark Collection [Ljosa et al., Nature Methods, 2012]."

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