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Dataset Information
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Dataset Name:
Metrics for growth responses of MDA-MB-231 and HME-1 cell lines to LINCS Pilot Phase TransCenter Project kinase inhibitors

Dataset Description:
This dataset presents calculated metrics (IC50, GI50, EC50, Hill coefficient and Einf) for the data in HMS-LINCS dataset #20215. The data in 20215 are measures of the sensitivities of two cell lines to the LINCS Pilot Phase TransCenter kinase inhibitors -- cells were treated with single drugs and cell number was measured after three days of drug exposure.

--Data in Package:
20216.txt

--Metadata in Package:
Small_Molecule_Metadata.txt
Cell_Line_Metadata.txt

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Center-specific Information
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Center-specific Name:
HMS_LINCS

Center-specific Dataset ID:
20216

Center-specific Dataset Link:
http://lincs.hms.harvard.edu/db/datasets/20216/

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Assay Information
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Assay Protocol:
1. Cells were plated at 2000 cells per well in 4x 384 well plates per cell line and grown for 24 hours.<br />
2. Three plates per cell line were treated with single drugs using the HP D300 drug dispenser.<br />
3. Immediately after treatment the untreated fourth plate for each cell line was fixed and stained by adding 20 l of fixative containing formaldehyde solution and Hoechst 33342 for a final concentration of 3% formaldehyde and 250 ng/ml Hoechst (no wash step). This plate was sealed and kept at 4C until day 3 of the assay.<br />
4. At day 3 the remaining plates were fixed, stained, and sealed as described in step 3.<br />
5. After 1 hour all plates were scanned with a PE Operetta high throughput plate scanner (10x WD lens with excitation peak at 380nm and emission peak at 445nm).<br />
6. Nuclei were counted using the Columbus software (module: 'Find Nuclei'; Method B; default parameters).<br />
7. The results were normalized by plate and the three replicates were averaged to yield the average relative cell count and the relative growth for each cell line, drug and concentration.<br />
8. Results at different concentration for a given drug and cell line are fitted with a sigmoidal curve to extract the IC50, GI50, EC50, Hill coefficient and Einf (see Fallahi-Sichani et al. Nat Chem Biol (2013) 9, p.708714). A null value is set for cases where IC50, GI50 cannot be interpolated.

Date Updated:
2016-09-09

Date Retrieved from Center:
11/13/2015

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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. For example, 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/
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