Scale Biosciences
High throughput combinatorial single-cell sequencing
Enhance your research capabilities with Scale Biosciences. We offer Scale Biosciences' Single-Cell RNA and CRISPR Guide Enrichment Kits as a service.
High throughput and cost-effective library preparation
Scale Biosciences solutions
Scale Biosciences' kits uses combinatorial indexing to barcode analytes within cells through a split-and-pool method. This approach enables the profiling of millions of nuclei or cells from any eukaryotic species without requiring specialized equipment. Thus, Single Cell Discoveries can multiplex thousands of samples or conditions in a single run resulting in high cell throughput and cost-effective library preparation.
In these protocols, the single-cell RNA sequencing uses three rounds of combinatorial barcoding to produce 3' polyA+ sequencing results from thousands to millions of cells. This workflow can also be integrated with single-cell CRISPR analysis. Its high throughput enables large-scale CROP-seq style PERTURB-seq experiments to be conducted more cost-effectively and with faster turnaround times.
Single Cell Discoveries offers Scale Biosciences' streamlined workflow compatible with automation, enhancing efficiency, reproducibility and throughput. This makes advanced single-cell studies accessible to a broader range of researchers, from academic labs to large-scale industrial applications.
Step 1
Consultation
Every project starts with one or more consultations to discuss the project set up. Our experienced PhD-level team, including our R&D scientists, discusses your biological question, sample type, planning, data analysis options, and other wishes.
Step 2
Sample Preparation
Create a single-cell suspension from your sample and either cryopreserve or fix the cells. Then, send your samples to our lab on dry ice. In the case of nuclei, the sample preparation depends on the project. If you are based near our lab in Utrecht, the Netherlands, it's possible to use freshly dissociated samples. Contact us to discuss this.
Step 3
Processing in Our Lab
Our experienced team performs the protocol in our lab. We sequence the libraries on our Illumina NovaSeq X Plus.. We’ll do multiple QC checks and keep you informed of the status of your project.
Step 4
Data Analysis
We will provide you with the raw data and our exploratory data reports. We can provide custom data analysis projects by our bioinformaticians.
Deliverables
As with all of our services, we provide ongoing support from our single-cell sequencing specialists. For each Scale Biosciences project, we provide the following.
- Regular updates during sample processing, including QC
- Raw sequencing data (FASTQ files)
- Gene count tables
- QC report of mapping results (UMIs per sample)
- An explanation from our data team about data quality metrics
- All raw sequencing data, results and reports are processed on EU servers, and securely encrypted using an AES (Advanced Encryption Standard) algorithm with a 256-bit key, before being delivered to the customers and archived.
Applications of Scale Biosciences
Single-Cell Transcriptomics
Scale Biosciences' single-cell RNA sequencing technology is designed to produce high-quality data by fixing and barcoding cells to create sequencing-ready libraries. This process supports in-depth studies of cellular phenotyping and tissue composition, providing insights into the complexity of biological systems.
Benefits of Scale Biosciences
High Throughput
Supports the preparation of up to 96 samples and 125,000-500,000 cells per run (with extended throughput kits). This makes large-scale experiments feasible and economical.
Cost Effectiveness
By reducing batch effects and enabling efficient scaling, Scale Biosciences lowers the overall cost of single-cell RNA sequencing.
Advanced Multiplexing
Scale Biosciences' patented ScalePlex technology allows for extensive sample multiplexing, even with low cell counts without complex preparation steps. This facilitates high throughput and flexible studies.
Low Multiplet Rate
Maintains a low multiplet rate of less than 5%, ensuring high quality data and reliable results.
CRISPR screening at scale
Learn about our 1 million-cell whole-genome CRISPR screen, conducted in collaboration with Illumina and Scale Biosciences. We discussed how Scale Biosciences' kits were instrumental in this project and how we can support your research.
FAQ
Cells or nuclei from eukaryotic species (only polyadenylated transcripts are captured, as the workflow relies on oligo-dT primers during the reverse transcription step).
At least 3 million cryopreserved cells/nuclei per sample, or 1.5 million cells/nuclei per sample if fixed using the Scale Biosciences fixation kit. If you have fewer cells/nuclei, please contact us to discuss options.
Samples can be shipped either cryopreserved or already fixed, specifically using the Scale Biosciences fixation kit according to the manufacturer’s instructions.
Preliminary QC reports of libraries/samples, cell filtering and calling, and generating count matrices.
Watch webinar
CRISPR screening at scale
In this webinar, you will learn:
- Why CRISPR screens require large number of cells
- How researchers are approaching these demands with the Scale Biosciences CRISPR Guide Enrichment Kit.
- How to achieve high throughput single-cell sequencing for projects that demand it