LabKey partners at the Allen Institute for Cell Science are doing things a little differently. Launched in 2014 with a contribution from founder and philanthropist Paul G. Allen, the Institute was formed to integrate diverse technologies and approaches to study the cell as an integrated system. They are asking fundamental questions about cellular behavior to better understand healthy and pathological cells. Data and tools developed by the Institute are made publicly available to researchers around the world.
The Allen Institute for Cell Science team uses genome editing to add fluorescent markers to proteins in key cellular machinery and uses light microscopy to study the organization of that machinery and how it changes. During the generation of genome edited cell lines, they conduct quality control steps, including genotyping, stem cell marker analysis, karyotype testing, deep sequencing, and image-based assays. They also generate clonal lines for each gene and ensure that the cell line is useful for long term experiments. This work requires tracking cells, cell lines, genes, and all other quality control components through approximately 40 workflow steps.
The Allen Institute for Cell Science uses LabKey Server to capture metadata and assay data on each gene, cell, cell line, clone, and vector at each stage in the workflow: information that was previously housed in spreadsheets and raw data files. The Institute relies on the integrated views and query-ability of their LabKey managed data to efficiently identify target cells/cell lines to explore. Their use of LabKey Server also allows them to track the status of each entity as it makes its way through the processing pipeline, as well as monitor their complete workflow.
By centralizing their data, the Allen Institute for Cell Science will be able to accelerate their analysis and use insights gathered about their workflow to optimize their operations.