Accessible and highly scalable single-cell RNA-Seq solution for mRNA capture, barcoding, and library prep without complex workflows or microfluidics
Assay time
Hands-on time
Input quantity
Illumina Single Cell 3' RNA Prep makes single-cell RNA-Seq (scRNA-Seq) accessible for more labs with an easy, scalable, and microfluidics-free workflow. Researchers can undertake larger and more varied multiomics studies without the budget or technology constraints of other single-cell approaches.
Illumina Single Cell 3' RNA Prep can easily scale with a wide processing range from hundreds to hundreds of thousands of cells. This increased cell throughput can reveal rare cell types. The assay is also flexible to run one sample or up to 96 samples in parallel with sample multiplexing.
Illumina Single Cell 3' RNA Prep offers high transcript and gene sensitivity with the high-quality data you expect from Illumina. The gentle isolation technique helps detect fragile cells that are often missed by other methods. The assay is compatible with custom single-cell measurements for expanded multiomic applications.
Illumina Single Cell 3' RNA Prep does not require expensive microfluidic equipment or labor-intensive protocols. You can conduct single-cell studies on your benchtop using a simple manual workflow with flexible stopping points.
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 using DRAGEN and Partek software.
| Assay time | ~15 hr from cell capture to library prep |
|---|---|
| Content specifications | Captures the coding transcriptome |
| Description | Single-cell mRNA capture, barcoding, and library prep with a simple manual workflow, high transcript sensitivity, and cost-effective scalability. |
| Hands-on time | 10 mins for cell capture |
| Input quantity | 100 to 200,000 cells |
| Instruments | NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, NextSeq 550Dx in Research Mode, NovaSeq X System, NovaSeq 6000Dx in Research Mode, NovaSeq 6000 System, NovaSeq X Plus System |
| Mechanism of action | PIPseq technology |
| Method | mRNA sequencing |
| Multiplexing | Up to 96-plex |
| Nucleic acid type | RNA |
| Specialized sample types | Blood, Not FFPE-compatible, Low-input samples, Bone marrow, Single cells |
| Species category | Any species, Mouse, Yeast, Zebrafish, Human |
| Strand specificity | Non-stranded |
| Technology | Sequencing |
| Variant class | Transcript variants |
Illumina Single Cell 3' RNA Prep includes both cell capture and library prep reagents. Choose the size kit to match the number of cells you want to assay. Kits are also available separately as Illumina Single Cell 3' RNA Capture and Illumina Single Cell Library Prep.
For multiplexing more than 8 samples per run, use Illumina Single Cell Unique Dual Indexes. To input single nuclei, use the Illumina Single Cell Nuclei Isolation Kit. For enrichment of custom RNA tag sequences, use the Illumina Single Cell Supplemental Enrichment and Amplification Kit.
New users should order the Illumina Single Cell Prep Starter Equipment for needed accessory equipment.
Neuronal tissues comprise a complex organization of diverse cell types that continuously reorganize and remodel throughout an organism’s lifetime. scRNA-Seq is a valuable tool to catalog the true diversity of neuronal cell populations with transcriptional sensitivity, providing insight into:
Cancer is a dynamic and diverse disease involving complex cell populations. Understanding the cell types and mutations that drive cancer requires sophisticated methods. scRNA-Seq has been a vital tool to:
The immune system is composed of a complex hierarchy of diverse cell types that work in concert to identify, target, and eliminate pathogens. scRNA-Seq allows researchers to:
Illumina Single Cell 3' RNA Prep
| Instrument | Recommended number of samples | Read length |
|---|---|---|
| NextSeq 2000 System | Samples per run: |
2 × 100 bp |
| NovaSeq 6000 System | Samples per run (dual flow cell): |
2 × 100 bp |
| NovaSeq X Plus System | Samples per run (dual flow cell): |
2 × 100 bp |
Single-cell and 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 analysis methods.
Single-cell sequencing allows researchers to understand drivers of cancer at the DNA, RNA, epigenetic, and protein levels within a single cell.
Use multiomics profiling to multiply discovery power and better connect genotype to phenotype.
Library Prep and Array Kit Selector
Find the right sequencing library preparation kit or microarray for your needs. Filter by method, species, and more. Compare, share, and order kits.
Single-cell mRNA capture and barcoding with PIPseq chemistry
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 scRNA-Seq data using DRAGEN and Partek software.
High-resolution scRNA-Seq at a scale of thousands of cells
Barcode rank plot (left) and barnyard scatter plot (right) showing effective separation of mixed culture of NIH3T3 (mouse) and HEK 293 (human) cell lines. 4106 cells captured using the Illumina Single Cell 3ʹ RNA Prep T2 kit with less than 5% multiplets.
High-resolution scRNA-Seq at a scale of tens of thousands of cells
Single-cell RNA-Seq for cryopreserved human peripheral blood mononuclear cells (PBMCs). UMAP of 31,613 cells captured using the Illumina Single Cell 3ʹ RNA Prep T20 kit resolves diverse immune cell populations.
High-resolution scRNA-Seq at a scale of hundreds of thousands of cells
Single-cell RNA-Seq for mouse brain nuclei from frozen tissue. UMAP analysis of 155,000 nuclei captured using the Illumina Single Cell 3ʹ RNA Prep T100 kit resolves diverse brain cell populations.
Illumina Single Cell 3' RNA Prep, T2 (8 samples, 2000 cells/sample)
20135689
Illumina Single Cell 3' RNA Prep, T2 (8 samples), includes Illumina Single Cell Library Prep plus reagents for single-cell mRNA capture, barcoding, and cDNA synthesis of up to 2000 cells per sample.
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Illumina Single Cell 3' RNA Prep, T10 (8 samples, 10,000 cells/sample)
20135691
Illumina Single Cell 3' RNA Prep, T10 (8 samples), includes Illumina Single Cell Library Prep plus reagents for single-cell mRNA capture, barcoding, and cDNA synthesis of up to 10,000 cells per sample.
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Illumina Single Cell 3' RNA Prep, T20 (4 samples, 20,000 cells/sample)
20135692
Illumina Single Cell 3' RNA Prep, T20 (4 samples), includes Illumina Single Cell Library Prep plus reagents for single-cell mRNA capture, barcoding, and cDNA synthesis of up to 20,000 cells per sample.
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Illumina Single Cell 3' RNA Prep, T100 (2 samples, 100,000 cells/sample)
20135693
Illumina Single Cell 3' RNA Prep, T100 (2 samples), includes Illumina Single Cell Library Prep plus reagents for single-cell mRNA capture, barcoding, and cDNA synthesis of up to 100,000 cells per sample.
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Illumina Single Cell Library Prep (8 reactions)
20132789
Illumina Single Cell Library Prep (8 reactions), used following Illumina Single Cell 3' RNA Capture.
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Illumina Single Cell 3' RNA Capture, T2 (8 samples, 2000 cells/sample)
20132790
Illumina Single Cell 3' RNA Capture, T2 (8 samples), for single-cell mRNA capture, barcoding, and cDNA synthesis of up to 2000 cells per sample, used prior to Illumina Single Cell Library Prep.
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Illumina Single Cell 3' RNA Capture, T10 (8 samples, 10,000 cells/sample)
20132791
Illumina Single Cell 3' RNA Capture, T10 (8 samples), for single-cell mRNA capture, barcoding, and cDNA synthesis of up to 10,000 cells per sample, used prior to Illumina Single Cell Library Prep.
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Illumina Single Cell 3' RNA Capture, T20 (4 samples, 20,000 cells/sample)
20132792
Illumina Single Cell 3' RNA Capture, T20 (4 samples), for single-cell mRNA capture, barcoding, and cDNA synthesis of up to 20,000 cells per sample, used prior to Illumina Single Cell Library Prep.
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Illumina Single Cell 3' RNA Capture, T100 (2 samples, 100,000 cells/sample)
20132793
Illumina Single Cell 3' RNA Capture, T100 (2 samples), for single-cell mRNA capture, barcoding, and cDNA synthesis of up to 100,000 cells per sample, used prior to Illumina Single Cell Library Prep.
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Illumina Single Cell Unique Dual Indexes (96 indexes, 96 samples)
20132788
Illumina Single Cell Unique Dual Indexes (96 indexes, 96 samples), optional accessory for use with the Illumina Single Cell Library Prep for high-plex pooling of libraries.
Illumina Nuclei Isolation Kit (4 samples)
20132795
Illumina Nuclei Isolation Kit (4 samples), optional reagents for nuclei isolation, washing, and resuspension for input into Illumina Single Cell 3' RNA Prep.
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Illumina Single Cell Supplemental Enrichment and Amplification Kit
20132794
Illumina Single Cell Supplemental Enrichment and Amplification (SEA) Kit, optional reagents for use with Illumina Single Cell 3' RNA Capture and Illumina Single Cell Library Prep for custom single-cell applications.
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Illumina Single Cell Prep Starter Equipment
20132796
Illumina Single Cell Prep Starter Equipment, one-time purchase accessory equipment required to prepare Illumina Single Cell 3' RNA kits and Illumina Single Cell Library Prep kits.
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Product
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Illumina Single Cell 3' RNA Prep uses PIPseq technology with pre-templated instant partitions (PIPs). PIPs can segregate complex cell mixtures into partitions with barcoded template particles that can be easily processed for single-cell applications such as single-cell RNA sequencing (scRNA-Seq).
Yes, our vortex mixer and dry bath are required for reliable results. The vortex mixer is engineered for consistent emulsification. The dry bath ensures precise temperature profiles; typical dry baths do not allow the quick temperature changes that are described in our lysis protocol.
Yes, using the Fluent DSP/Methanol Fixation demonstrated protocol for cells or nuclei. Paraformaldehyde (PFA) fixation is not compatible currently.
No, only 3' mRNA capture is available currently.
Reagents for the NextSeq 1000/2000 System feature easy-to-use cartridges and multiple flow cell configurations for flexible sequencing options.
Reagent kits for the NovaSeq X Series include a reagent cartridge, buffer cartridge, flow cell, lyo insert, pre-load buffer, and library tube strip.
Reagent kits for the NovaSeq 6000 System consisting of ready-to-use pre-filled reagent cartridges and flow cells.
Maximize genomic insights with DRAGEN secondary analysis, learn about the latest updates, read FAQs, and find product support.
A rapid, cost-effective workflow for accurate, unbiased detection of the protein-coding transcriptome with precise measurement of strand information.
A fast, integrated workflow for preparing libraries for use in a wide range of sequencing applications.
A fast, integrated workflow for producing enriched and indexed sequencing libraries from a broad range of sample types and RNA input quantities.
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