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

@article{,
title= {Human MCF7 cells – compound-profiling experiment (BBBC021v1)},
keywords= {Medical, Biology},
author= {The Broad Institute},
abstract= {![](https://i.imgur.com/nilVHAT.png)

![](https://i.imgur.com/8dcAHs0.png)

### 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:

```
TableNumber
ImageNumber
Image_FileName_DAPI
Image_PathName_DAPI
Image_FileName_Tubulin
Image_PathName_Tubulin
Image_FileName_Actin
Image_PathName_Actin
Image_Metadata_Plate_DAPI
Image_Metadata_Well_DAPI
Replicate
Image_Metadata_Compound
Image_Metadata_Concentration
```

### 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:

```
compound
concentration
moa
```

### 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]."

},
terms= {},
license= {},
superseded= {},
url= {https://data.broadinstitute.org/bbbc/BBBC021/}
}