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Advancing the field of in vivo genomic recording through the development of computational pipelines and methods.
The Seattle Hub for Synthetic Biology is a collaboration between Allen Institute, Chan Zuckerberg Initiative and the University of Washington.
Goals and Approach
The Read team at the Seattle Hub for Synthetic Biology is working to advance the field of in vivo genomic recording by developing computational pipelines and methods to characterize lineage relationships and biological signaling between cells across various tissues. We aim to develop open, reproducible, and scalable bioinformatics workflows for the analysis of recording experiments. From our workflows and analyses, we aim to understand and characterize the mechanisms underlying prime editing mediated genomic recording to build the most informative and capable genomic recorder. Through our work, we hope to advance the field’s understanding in this area and unlock a new era of in vivo genomic recording.
We develop open, reproducible, and scalable bioinformatics workflows for the data processing and analysis of prime editing mediated recording experiments in both mouse embryonic stem cell cultures and mouse models. The data going into our pipelines includes short and long read next-generation sequencing data, from both bulk and single-cell genomics experiments.
From data generated in the lab, we track cell lineages and biological signaling events by reading out the identity and sequential order of DNA barcodes that mark these events. By integrating many synthetic DNA TAPE constructs into cells, we have a large capacity to record cell lineage and biological signaling over many generations of cell divisions. The datasets we generate will enable the development of novel computational approaches towards whole organism lineage tracing.
