Our functional
genomics platform
maps the central dogma

From CRISPR screens to nascent RNA sequencing, we deploy cutting-edge genomics technologies to map biology and understand disease.

Navigating complex biology requires input from many different assays

Our team includes world experts in functional genomics assay development and optimization.

Nascent RNA Sequencing

Nascent RNAs are a population of RNAs that are being actively transcribed by RNA polymerase. They can be leveraged to study mechanisms of transcription as well as characterize thousands of non-coding RNAs that can't be detected by traditional assays. Techniques like GRO-seq, PRO-seq, and NET-seq were developed to capture these molecules, but they're challenging and time consuming. We’ve developed an automated workflow to solve this problem.

CRISPR Screens

CRISPR represents an exciting new technology to edit the genome with unparalleled precision. With the development of pooled guide RNAs, we can create thousands of cellular genotypes, expose them to selective pressures, and identify new drivers of signaling cascades, cancer growth or cell type differentiation. Like many sequencing technologies, CRISPR screens are demanding and costly. We’ve developed new methods to make CRISPR screens scalable.

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Open Chromatin Profiling

Gene expression is controlled by the exposure of DNA to transcription factor binding motifs. Profiling open vs closed chromatin can help identify spots of the genome that are functional and critical for defining cell state. By combining techniques like ATAC-seq with our scalable PRO-seq technology, we’re driving a deeper understanding of gene regulatory networks in cancer.

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mRNA Profiling

With ATAC-seq and PRO-seq integrated into our platform, we complete the central dogma by including mRNA profiling. RNA-sequencing quantifies the abundance of messenger RNAs in a cell. When combined with PRO-seq, we can reverse engineer RNA half life, co-transcriptional splicing dynamics and the effect that critical transcription factors are playing in this process.

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Single-Cell Sequencing

Many hundreds of different cell types orchestrate our body’s physiology. Arpeggio employs single-cell RNA sequencing to discover new cell types implicated in diseases arising from the immune system. We are developing precise methods to isolate nascent RNA transcripts from a single cell.

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Large-Scale Drug Treatments

Mapping the regulatory network is often easier in the context of drug perturbations. How a cell type responds to different perturbations can illuminate cell type identity and the signaling cascades that underlie it. We are developing robotic solutions to perform massive compound treatments within the context of functional genomics.

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Select Partners:

Featured Collaborators

Intrinsic Medicine:
Drug Co-development

With Intrinsic Medicine, we’re systematically unlocking the therapeutic potential of oligosaccharides. With candidates selected from a unique evolutionarily selected and conserved library, this exciting new class of medicines has shown disease-modifying efficacy in multiple autoimmune and inflammation-related disease models with exceptionally clean toxicology. New biology of inflammation, cell modulation, and disease applications have been discovered by studying these candidates within the context of our functional genomics platform.

Treventis Corporation:
Target Discovery

Gain of function mutations in P53 drive cancerous cell growth, but little is known about their mechanism and how to develop new therapies to inhibit them. We’ve collaborated with the Treventis Corporation to apply our platform to mutant P53 cells. We’ve characterized new mutant P53 binding dynamics and a new therapeutic target for this specific cancer genotype.

Forma Therapeutics:
Drug Mechanism of Action

Our functional genomics platform can very quickly identify the mechanism of action of a compound. By looking at early changes in the transcriptome, we can find the primary response to any compound and machine learning can reverse engineer in many cases the target of that drug. With Forma Therapeutics, we defined a clearer understanding of the translational utility of its small molecule pipeline of therapeutics targeting cancer and other serious diseases.

Arpeggio Analytics

Making genomic analysis easy

Our cloud-based web software provides an end-to-end solution for genomic analysis. We make it easy to analyze thousands of datasets with drag-and-drop features, explore live graphics, and apply advanced machine learning to identify critical nodes in gene regulatory networks.

Analytics Software

Contact Us

Have questions? Interested in partnering with Arpeggio? Let us know.

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