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

BBBC021 (58 files)
BBBC021_v1_compound.csv 8.18kB
BBBC021_v1_image.csv 3.97MB
BBBC021_v1_images_Week1_22123.zip 839.44MB
BBBC021_v1_images_Week1_22141.zip 851.40MB
BBBC021_v1_images_Week1_22161.zip 841.37MB
BBBC021_v1_images_Week1_22361.zip 854.60MB
BBBC021_v1_images_Week1_22381.zip 861.58MB
BBBC021_v1_images_Week1_22401.zip 874.85MB
BBBC021_v1_images_Week2_24121.zip 813.32MB
BBBC021_v1_images_Week2_24141.zip 812.95MB
BBBC021_v1_images_Week2_24161.zip 817.95MB
BBBC021_v1_images_Week2_24361.zip 819.82MB
BBBC021_v1_images_Week2_24381.zip 744.17MB
BBBC021_v1_images_Week2_24401.zip 800.66MB
BBBC021_v1_images_Week3_25421.zip 871.46MB
BBBC021_v1_images_Week3_25441.zip 857.91MB
BBBC021_v1_images_Week3_25461.zip 866.10MB
BBBC021_v1_images_Week3_25681.zip 872.82MB
BBBC021_v1_images_Week3_25701.zip 872.58MB
BBBC021_v1_images_Week3_25721.zip 879.70MB
BBBC021_v1_images_Week4_27481.zip 821.23MB
BBBC021_v1_images_Week4_27521.zip 900.82MB
BBBC021_v1_images_Week4_27542.zip 842.01MB
BBBC021_v1_images_Week4_27801.zip 887.88MB
BBBC021_v1_images_Week4_27821.zip 869.27MB
BBBC021_v1_images_Week4_27861.zip 859.01MB
BBBC021_v1_images_Week5_28901.zip 855.93MB
BBBC021_v1_images_Week5_28921.zip 871.72MB
BBBC021_v1_images_Week5_28961.zip 842.79MB
BBBC021_v1_images_Week5_29301.zip 852.25MB
BBBC021_v1_images_Week5_29321.zip 863.88MB
BBBC021_v1_images_Week5_29341.zip 873.15MB
BBBC021_v1_images_Week6_31641.zip 820.70MB
BBBC021_v1_images_Week6_31661.zip 858.47MB
BBBC021_v1_images_Week6_31681.zip 800.43MB
BBBC021_v1_images_Week6_32061.zip 805.25MB
BBBC021_v1_images_Week6_32121.zip 821.45MB
BBBC021_v1_images_Week6_32161.zip 736.92MB
BBBC021_v1_images_Week7_34341.zip 848.89MB
BBBC021_v1_images_Week7_34381.zip 807.29MB
BBBC021_v1_images_Week7_34641.zip 878.01MB
BBBC021_v1_images_Week7_34661.zip 871.25MB
BBBC021_v1_images_Week7_34681.zip 869.46MB
BBBC021_v1_images_Week8_38203.zip 784.99MB
BBBC021_v1_images_Week8_38221.zip 821.32MB
BBBC021_v1_images_Week8_38241.zip 765.06MB
BBBC021_v1_images_Week8_38341.zip 781.85MB
BBBC021_v1_images_Week8_38342.zip 770.98MB
BBBC021_v1_images_Week9_39206.zip 781.36MB
BBBC021_v1_images_Week9_39221.zip 790.10MB
BBBC021_v1_images_Week9_39222.zip 771.02MB
BBBC021_v1_images_Week9_39282.zip 730.87MB
BBBC021_v1_images_Week9_39283.zip 779.10MB
BBBC021_v1_images_Week9_39301.zip 725.13MB
BBBC021_v1_images_Week10_40111.zip 886.67MB
BBBC021_v1_images_Week10_40115.zip 855.66MB
BBBC021_v1_images_Week10_40119.zip 829.93MB
BBBC021_v1_moa.csv 4.40kB
Type: Dataset
Tags:Medical, Biology

Bibtex:
@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/}
}


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Best Time 1 hours, 16 minutes, 12 seconds
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