The data we collect in HMS LINCS is multi-factorial and involves a variety of biochemical, image-based and phenotypic assays. Although the individual assays used in the HMS LINCS Center are quite common in conventional cell-biological studies, our goal is to collect “systematic” data sets in which the assays are performed in a quantitative and reproducible way on many samples, with many perturbing small molecules (or other perturbagens), and in many cell lines.
Each of our six types of data will be described using a common set of metadata tags. By searching the HMS LINCS Data Repository it will eventually be possible to identify all types of data corresponding to a particular cell line, perturbagen or assay.
HMS LINCS data types
- Information about perturbagens including compound structures, quality control data, and curated information about known targets and active concentrations.
- Drug-target interaction data on the binding of small molecule drugs to kinases present in cell extracts, and related data on the ability of drugs to inhibit recombinant kinases (the KINOMEscan and the KiNativ assays).
- Biochemical response data on the abundance and state of modification of 20-100 signaling proteins carried out using bead-based xMAP assays, Western blotting and reverse phase lysate arrays.
- Growth inhibition data collected at MGH/Sanger Institute on the growth inhibition of cells over a three-day period based on quantifying DNA content.
- Microscopy data on fixed and live cells to measure protein modification and localization, and to score mitotic state, cell growth, apoptosis, and cell motility over a 72 hr period.
- Transcriptional response data on the abundance of 1000 landmark mRNAs in perturbed cells (collected in collaboration with Broad LINCS Center).