Traditional high-throughput drug screening often relies on visual markers that are challenging to quantify and limited in scope. In contrast, RNA sequencing-based screening offers transcriptome-wide quantitative insights, enabling the discovery of affected genes and pathways with greater precision. In the previous blog, we explored how high-throughput screening accelerates drug discovery by enabling the simultaneous testing of thousands of compounds.
Performing RNA sequencing (RNA-seq) on thousands of samples allows us to understand a drug's Mode-of-Action (MoA) comprehensively. The identification of common and unique gene expression patterns enhances the precision and reliability of the drug.
Discovery-seq is our novel and cost-effective method to perform high-throughput 3' bulk RNA sequencing. As the workflow is highly automated, we can sequence thousands of samples within one experiment, making it economical. It is designed to accelerate drug and target discovery pipelines by enabling researchers to study how drugs influence cells at the transcriptome level during large-scale perturbation experiments.
In this blog, we dive into more detail on how Discovery-seq works and how it can apply to your next screening experiment.
Discovery-seq: High throughput RNA sequencing
Discovery-seq is an in-house developed method to facilitate high-throughput RNA sequencing of thousands of samples. Single Cell Discoveries exclusively offers the Discovery-seq method.
Discovery-seq exploits the same molecular biology as our current single-cell and bulk RNA sequencing methods. This makes the Discovery-seq method different from the more known DRUG-seq.
We aimed to develop a method with higher accuracy and lower cost. We have improved the sensitivity in the Discovery-seq protocol and removed the PCR bias present in DRUG-seq.
Discovery-seq also greatly lowers costs. It offers a 10-fold price reduction compared to traditional RNA-seq methods. This makes transcriptomic readouts easier to access for high-throughput screens.
This cost efficiency makes Discovery-seq a great choice for screening compounds. It helps identify drug candidates and study mechanisms of action. Discovery-seq is also useful for conducting target discovery screens with gene changes.
Researchers can ideally integrate Discovery-seq into existing screening workflows. We can evaluate screening plates after viability assays, cell painting, or high-content screening. Once the data has been acquired, clients wash the cells, followed by snap freezing and submitting them to us to perform Discovery-seq. We can integrate multimodal data to gain a better understanding of the impact of your experimental conditions.
Workflow of Discovery-seq
Clients utilizing our Discovery-seq services send us washed and frozen cells in 384-well or 96-well plates. For optimal results, we seed plates at a density of 3,000-10,000 cells per well. Our Discovery-seq protocol removes the need for RNA extraction. It uses a direct in-well plate lysis method to process cells.
Barcoding, early multiplexing, and automation enable cost-effective and time-efficient processing of many samples in one experiment. A standardized workflow using multiple robots and automatized steps also ensures high-throughput and high-quality results.
Projects will include sequencing at a read depth of 1-2 million reads per sample, which recovers around 12,000 genes per sample. Read depth can be increased up to 4 million reads/per sample if required.
What materials are compatible with Discovery-seq?
Discovery-seq is compatible with a wide range of cell culture systems and organoid models. This method provides the flexibility to uncover effects regardless of cell viability or visual detection limitations.
Learn how to leverage Discovery-seq for transcriptomic phenotyping of organoids in this tech note.
Applications of Discovery-seq
High-throughput RNA sequencing in small compound drug screens enables the simultaneous analysis of multiple compounds' effects on gene expression. This accelerates drug discovery by quickly identifying promising candidates. It also provides valuable insights into potential side effects and therapeutic targets.
Our Discovery-seq service supports projects that require high-throughput transcriptomics for drug discovery. It provides a cost-effective and scalable way to process many bulk RNA sequencing samples. For instance, scientists can leverage this technology to study how gene expression changes under different environmental conditions or genetic modifications.
Discovery-seq is particularly well-suited for profiling exposure to various perturbations, such as high-throughput drug screening or CRISPR/siRNA screens for target discovery. With this service, researchers can obtain transcriptomics data for thousands of compounds in a single experiment, streamlining the identification of therapeutic targets.
Discovery-seq can reveal unbiased whole transcriptome data, uncovering complex drug responses and mechanisms of action.
For projects with fewer samples, our regular bulk RNA sequencing service may be a better fit.
Please click here to read more about the results from trichostatin A dosing in our tech note.
Deliverables
Our standard pipeline provides you with an exploratory report. This report helps assess the experiment's performance and interpret the results. Please find an example of our Discovery-seq data report here.
How can you get started with Discovery-seq?
Discovery-seq is perfectly suited for integration into existing screening workflows. Screening plates can be assessed using viability assays, cell painting, or high-content screening. After data acquisition, the process is straightforward: wash the cell pellets or organoids, snap freeze them, and submit them to us for Discovery-seq. This allows for the integration of multimodal data, providing a comprehensive understanding of the impact of your experimental conditions.
Please contact us for more information on Discovery-seq or download the information guide below.
Information Guide Discovery-seq
Discover our Discovery-seq service
Download our information guide to access an overview of Single Cell Discoveries, explore our Discovery-seq service, learn how to get started, and gain more valuable insights.
