Reveal cell-level insights, explore complex biology, and discover new biomarkers with scalable, flexible single-cell sequencing workflows
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Single-cell RNA sequencing (scRNA-Seq) provides a high-resolution view into gene expression within complex tissues. Single-cell sequencing solutions from Illumina make this transformative approach more accessible than ever before, with scalable microfluidics-free workflows. Using novel PIPseq (particle-templated instant partition sequencing) chemistry, Illumina single-cell solutions deliver high performance and ease of use, bringing single-cell sequencing capabilities to more labs.
PIPseq chemistry offers a scalable, vortexer-based workflow that overcomes the budget or technology constraints of other single-cell approaches. By enabling highly sensitive and precise transcript detection, this innovative method expands discovery power for both new and experienced single-cell researchers.
Illumina Single Cell 3′ RNA Prep opens doors to new discoveries by enabling sensitive detection of transcripts from fragile cells and complex tissues like solid tumors and myelin-rich tissues like brains, which can be challenging to resolve using microfluidics-based techniques.
This study from UCSD used PIPseq to classify more than 30 retinal ganglion cell-like neuron subtypes at single-cell resolution, which is critical to understanding retinal regeneration in optic nerve disorders like glaucoma.
This UCSF study used PIPseq to perform single-cell CRISPR screening studies and reveal the impacts of gene perturbations across the transcriptome at single-cell resolution.
In this webinar, Sheila Dodge from the Broad Institute talks about how her research team used Illumina Single Cell 3′ RNA Prep to scale their Perturb-seq experiments, allowing them to process more than 5 million cells in just 5 days and unlock genome-wide CRISPR insights.
The ease with which we have been able to generate large numbers of single cells for challenging neuronal samples is amazing. Sequencing quality, including genes detected, doublet errors, and mitochondrial contamination levels are exceptional, and on par with other methods.
I have no doubt that this approach utilizing PIPseq will be an impactful addition to the laboratory repertoire for any researcher.
Explore how researchers are using Illumina single-cell sequencing in immunology, cancer research, neurobiology, plant biology, and more
A UCSF study used Illumina Single Cell 3′ RNA Prep on cocultured macrophages and fibroblasts to reveal important crosstalk between these cells that is necessary for injury-associated fibrosis.
Another UCSF study used Illumina Single Cell 3′ RNA Prep on mixed phenotype acute leukemia samples to examine the diversity of cells present within chemotherapy-resistant subsets. PIPseq revealed cell profiles that were not detected by standard immunotyping.
A study from NYU used Illumina Single Cell 3′ RNA Prep for a large scale single-cell study (100,000 cells/sample) to examine inflammatory genes within the brains of multiple mouse species and genotypes.
Researchers from UCSF and Memorial Sloan Kettering Cancer Center used a modified PIPseq-based method to isolate and characterize long-term hematopoietic stem cells, a rare and heterogenous bone marrow population that is difficult to capture successfully using existing methods.
Scientists at the Max Planck Institute and University of Georgia combined mass spectrometry with Illumina Single Cell 3′ RNA Prep to identify and quantify the concentrations of 16 metabolites across four natural product classes in individual cells from various plant tissues.
Single-cell data can be analyzed and visualized using DRAGEN secondary analysis and Illumina Connected Multiomics. These powerful software tools enable researchers to place single-cell results into biological context and uncover meaningful insights.
Single-cell sequencing data are analyzed using the DRAGEN Single Cell RNA pipeline, which is optimized to process raw sequencing data generated using Illumina Single Cell 3' RNA Prep. This powerful tool aligns and maps reads to a reference and performs position sorting followed by gene matching. After error correction, a unique molecular count per cell is used to filter cells and generate a final expression matrix. The results are then visualized in Illumina Connected Multiomics.
Illumina Connected Multiomics is a streamlined, user-friendly software for exploring single-cell sequencing data. Maximize insights from single-cell assays with built-in tools for filtering, normalization, dimensionality reduction, clustering, cell classification, differential expression, and pathway analysis. Annotate results with phenotypic metadata for richer biological context and leverage interactive 2D and 3D visualizations to integrate results for comparative analysis.
Unlike droplet-based systems, PIPseq chemistry uses emulsion-based particle-templated instant partitions (PIPs) to isolate and barcode individual cells. This approach eliminates the need for complex microfluidic instrumentation while maintaining high capture efficiency.
During sample preparation, the cell suspension of interest is mixed with template particles and oil and segregated into templated emulsions by vortexing. Cells in the emulsions are then lysed and the mRNA is captured by the barcoded template. Captured transcripts are reverse transcribed into cDNA and single-cell libraries are prepared and sequenced on Illumina NGS systems.
With 3′ RNA sequencing, Illumina Single Cell Prep (ISCP) T100 kits can process 5X as many cells in a single reaction for the same price as the leading single cell alternative 3'RNA kit (LSCA), allowing researchers to identify more unique cell types at lower cost.1
Illumina Single Cell 3' RNA Prep enables single-cell mRNA capture, barcoding, and library prep without complex workflows or microfluidics. Combined with Illumina sequencing and informatics solutions, Illumina Single Cell 3' RNA Prep provides a flexible and scalable workflow that makes high-performance single-cell RNA sequencing accessible for more labs.
Create templated emulsions using a vortex mixer to capture and barcode single-cell mRNA.
Generate cDNA and prepare single-cell libraries for sequencing.
Sequence on an NGS system to match the scale of your study.
Analyze and visualize single-cell data.
Discover the full single-cell sequencing workflow from tissue prep to data analysis in one resource. This 33-page eBook is packed with technical tips, workflow insights, and real-world recommendations to help you plan with confidence.
Your email address is never shared with third parties.
Revolutionizing single-cell sequencing
Download the eBook to explore Illumina Single Cell 3′ RNA Prep chemistry. Learn how it reduces costs, simplifies workflows, and delivers high-quality libraries for a more complete view of your tissue.
Your email address is never shared with third parties.
Accelerate single-cell studies with Illumina Connected Multiomics
Download the flyer to see how Illumina Connected Multiomics scales single-cell studies. Integrate multiomic data, visualize cell relationships, and accelerate discoveries with Illumina tools and DRAGEN analysis.
Single cell bioinformatics for researchers
Explore the power of single-cell bioinformatics in this on-demand webinar. Learn key analysis steps, cell typing, and how to interpret visualizations like tSNE and UMAP.
High-throughput single-cell CRISPR prep makes gene editing a reality
At AGBT 2025, Illumina scientists present a breakthrough method for interrogating the gene expression of individual cells.
Unlocking precision: The power of PIPseq V in scRNA-Seq
This on-demand webinar shows how PIPseq V advances single-cell sequencing with accurate, accessible insights. Presenters share real data and emerging possibilities in genomic research.
Single-cell and ultra-low-input RNA-Seq
With single-cell RNA-Seq, you can study cellular differences often masked by bulk sampling. Explore high- and low-throughput single-cell sequencing methods.
Single-cell sequencing powered by NGS can examine the genomes or transcriptomes of individual cancer cells, providing a high-resolution view of cell-to-cell variation.
Illumina spatial transcriptomics enables high-resolution, sequencing-based whole-transcriptome analysis in intact tissue sections.
Combine data from genomics, transcriptomics, epigenetics, and proteomics to better connect genotype to phenotype.
Advances in RNA-Seq library prep are revolutionizing the study of the transcriptome. Our enhanced RNA sequencing library prep portfolio spans multiple types of sequencing studies. These solutions offer rapid turnaround time, broad study flexibility, and sequencing scalability.
Discover how PIPseq chemistry and the Illumina Single Cell 3' RNA Prep can accelerate your research. Connect with our specialists to find the best fit for your applications.
Your email address is never shared with third parties.
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