blog

Multiplet rates explained: What every scRNA-seq researcher should know

Laura DeMare — Tue, 22 Jul 2025 20:10:22 GMT

Singlecell RNA sequencing (scRNA-seq) has revolutionized our ability to study cellular heterogeneity and gene expression at unprecedented resolution. However, one of the technical challenges that can compromise data quality and waste precious sequencing resources is the formation of multiplets. Understanding multiplets, how they arise, and their impact on experimental design is crucial for any researcher embarking on singlecell studies.

Partnering with Researchers on Single Cell Genomics Projects

Laura DeMare — Mon, 07 Jul 2025 21:27:30 GMT

At Scale, we believe the best science happens through partnership. We sat down with our Services Team lead, Claire Fraser, to discuss her journey into single cell genomics, the comprehensive services offered by Scale, and what makes working with researchers so rewarding.

Decoding Biology at the Single Cell Level: Why DNA Methylation Is the Next Frontier

Laura DeMare — Tue, 29 Apr 2025 17:07:52 GMT

Single cell analysis is transforming biology - but what lies beyond RNA? Single cell analysis has emerged as a revolutionary technology, fundamentally changing our understanding across diverse areas in biology. While most breakthrough discoveries have been powered by single cell RNA sequencing, new frontiers are opening as additional single cell -omics methods become more accessible and robust.

One particularly promising yet underutilized approach is single cell DNA methylation. This powerful epigenetic profiling method offers unique insights impossible to obtain through transcriptomics alone. Let's explore what makes single cell methylation so valuable and examine some research examples that demonstrate its unique capabilities.

Towards Virtual Tissue Models: A Conversation with Dr. Barbara Treutlein on Organoids, AI, and High-Throughput Single Cell Screening

Laura DeMare — Wed, 12 Mar 2025 16:47:43 GMT

At the forefront of cell biology and tissue engineering, Dr. Barbara Treutlein is pioneering ways to understand and model the human brain. As a professor at ETH Zurich and winner of the 100 Million Cell Challenge, alongside collaborator Dr. Fabian Theis, she's combining innovative approaches to study brain development underlying mechanisms of disease with single cell analysis. In this insightful conversation, Dr. Treutlein shares her excitement of using organoids to model the human brain, harnessing AI to accelerate laboratory discoveries, and how massive-scale single-cell experiments are bringing us closer to complete virtual models of human tissues.

Improving drug discovery using genetic diversity with Drew Neavin

Laura DeMare — Thu, 23 Jan 2025 00:29:01 GMT

We’re excited to highlight one of the winners of the 100 Million Cell Challenge, Dr. Drew Neavin. Dr. Neavin is an investigator at the Garvan Institute of Medical Research. She recently sat down with us to discuss her innovative research on adverse drug reactions, how large-scale single cell analysis will be instrumental for unlocking genetic factors behind drug toxicity, and her ambitious upcoming project on QuantumScale.

The Complex Journey of Drug Development

Archana Bettadapur — Tue, 14 Jan 2025 23:58:57 GMT

The impact of massive multiplexing on drug development is transformative. Historically, drug screening has faced a crucial limitation: researchers must choose between testing many drugs or getting detailed cellular responses, but rarely both. ScalePlex’s massive multiplexing technology shatters this trade-off, allowing us to see the entire biological picture at once.

Before a single pill reaches a patient's hands, it undergoes a complex journey spanning roughly 10-15 years and costs exceeding billions of dollars. This journey begins with target discovery to identify the molecular mechanisms driving disease and testing of thousands of compounds to find those that effectively interact with the target.

These foundational experimentation steps determine the success of preclinical testing and clinical trials, with 90% of the latter ultimately failing due to suboptimal target selection.

Breaking the Single Cell Bottleneck with ScalePlex

Archana Bettadapur — Mon, 16 Dec 2024 21:58:29 GMT

As researchers hunger to explore more cellular landscapes, the traditional scRNA-seq workflow becomes a financial and logistical labyrinth. More samples mean exponentially rising costs, more complex protocols, and diminishing returns. It's like wanting to understand an entire ecosystem but being constrained to studying just a few square meters. Enter a groundbreaking multiplexing kit that shatters these limitations. This technological breakthrough doesn't just incrementally improve research – it reimagines what's possible. By scaling sample throughput from dozens to potentially thousands of samples, researchers can now map cellular diversity with unprecedented breadth and depth.

The next big leap in single cell: Introducing Quantum Barcoding

Laura DeMare — Thu, 21 Nov 2024 01:17:48 GMT

In the rapidly evolving landscape of single cell RNA sequencing, researchers still face technological limitations that pose challenges to scalability, efficiency, and cost-effectiveness. Scale Bio's novel Quantum Barcoding technology represents a fundamental rethinking of how we approach single cell analysis, greatly expanding the number of cells that can be analyzed with massively parallel barcoding approaches, while simultaneously improving workflow efficiency, for the most user-friendly single cell workflow.

Why your scRNA-seq project deserves more cells and samples

Laura DeMare — Mon, 28 Oct 2024 17:17:46 GMT

Single cell RNA sequencing (scRNA-seq) is rapidly advancing our understanding of complex biological phenomena – from the organization and function of cells within a tissue, cellular functions that go awry in disease, to the diversity of our immune systems – by analyzing the unique transcriptomic signatures of individual cells. Yet, despite its transformative potential, we've only scratched the surface of what scRNA-seq can reveal. The cells and samples analyzed to date represent just a fraction of the vast cellular universe waiting to be explored. In this article, we'll dive into the exciting possibilities that arise when we dramatically scale up our single cell projects, both in the sheer number of cells analyzed and the diversity of samples studied.

NovaSeq X Loading: Navigating Barcode Error Rates for scRNA-seq

Austin Holmes — Mon, 21 Oct 2024 20:11:04 GMT

The transition to NovaSeq X technology has brought both exciting opportunities and new challenges for single cell RNA sequencing. As many labs adopt this platform, we've observed a common phenomenon: increased barcode error rates that warrant careful consideration. To help our community optimize their sequencing runs, we conducted a systematic investigation of loading concentrations and their impact on sequencing quality. Here's what we discovered and what it means for your experiments.