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Dataset Information
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Dataset Name: 
MGH (CMT) Growth Inhibition Assay Protocol - DNA Staining

Dataset Description: 
The CMT platform uses a DNA stain (Syto60) or Resazurin based assay to determine cell viability following compound treatment (either 3-dose or 9-dose concentration range).

3-dose tests: A single cell line is seeded in each 96 well plate and assayed against a panel of compounds. In each 96 well plate, 8 test compounds are assayed at three different doses in triplicate (72 wells total). In each plate, 18 Control wells are treated with DMSO only (no test compound), and 6 wells contain no cells. After a 72 hour incubation, the relative cell number in each well is determined using bulk fluorescence measurement (Syto60). For this assay cells are fixed before staining. Cell viability corresponds to the signal in each compound-treated well relative to the averaged signal for the Control (DMSO treated) wells for each cell line. - Cell Density at seeding time: variable (~15% confluence) to ensure continuous growth during compound treatment. - Doses: 3 concentrations, 10 fold apart. Actual concentrations are provided and vary for each compound. Concentrations used are based on published literature and pre-screening work done at CMT to estimate potency. - Compound treatment duration : 72h.

9-dose tests: A single cell line is seeded in each 384 well plate and assayed against a panel of compounds. In each 384 well plate, 4 to 8 test compounds are assayed at nine different doses. In each plate, 42 Control wells are treated with DMSO only (no test compound), and 32 wells contain no cells. After a 72 hour incubation, the relative cell number in each well is determined using bulk fluorescence measurement (either resazurin or Syto 60). For the Syto 60 assay, cells are fixed before staining. We report an average FI : Control Ratio for each cell line and compound concentration. This ratio is calculated by dividing the average FI for each condition by the averaged signal in Control (DMSO treated) wells. Conditions where more cells are viable have a high ratio; conditions where fewer cells are viable have a lower ratio. - Cell Density at seeding time: variable (~15% confluence) to insure continuous growth during compound treatment. - Doses: 9 concentrations, 2-fold apart. Actual concentrations are provided and may vary among compounds. Concentrations used are based on published literature and pre-screening work done at CMT to estimate potency. - Compound treatment duration: 72h. 

Dataset Contents:
1) dataset_20010.csv
Location: In package
Description: Data file

2) Small_Molecule_Metadata.txt
Location: In package
Description: Metadata file 1

3) Cell_Line_Metadata.txt
Location: In package
Description: Metadata file 2


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Center-specific Information
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Center Name: 
CMT-MGH

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Assay Information
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Assay Name: 
Fluorescence Imaging Cell Growth Inhibition Assay

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Metadata Information
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Metadata information regarding the entities used in the experiments is included in the accompanied metadata. A metadata file per entity category is included in the package. The metadata for all the cell lines that were used in the dataset are included in the Cell_Lines_Metadata.txt file.

Descriptions for each metadata field can be found here: http://www.lincsproject.org/data/data-standards/