Description
Dissociate your fresh, frozen, and archival FFPE samples with a fully automated platform that delivers consistent, high-quality nuclei and cell preps from inputs as low as 2 mg or 50 µm curls
Singulator 200+ Platform Generates High-Quality snRNA-seq Data From FFPE Samples, Enabling New Discoveries
- Both Xenium and snRNA-seq data identified the same major cell types via UMAP, demonstrating consistency across platforms.
- Xenium data showed overlapping immune signatures, while snRNA-seq revealed discernable differences and allowed spatial imputation of immune cell locations.
Data adapted from: Haviv, D., Remšík, J., Gatie, M. et al. Nat Biotechnol 42, 843–852 (2024) .
Proven the Number One Method for Reproducibility and Precision
Published data comparing Singulator™ to alternative methods proved across all metrics that Singulator is the best method for tissue dissociation. It consistently produces high quality results demonstrated in over 80 tissue types from fresh, frozen, OCT, and FFPE materials. From input amounts as small as 2 mg to customizable protocols, the Singulator handles your samples quickly and with little to no clean up.
Choose Your Perfect System
Compare capabilities to find the right automated dissociation solution for your lab.
Singulator 200+ System - Includes one reagent module, two 250 mL bottles for water and waste, one blue water bottle cap assembly, one red waste bottle cap assembly, one green Nuclei Isolation Reagent bottle cap assembly, one yellow Nuclei Storage Reagent bottle cap assembly, two Decontamination cartridges V2, one computer keyboard, one tablet computer with software, and one specified power supply. System also includes one year warranty.
Troubleshooting neurodegenerative disease FFPE challenges
Problem: snRNA-seq data from Alzheimer's hippocampus shows predominantly microglia with few neuronal clusters
Solution: This pattern often reflects processing bias rather than disease biology. Manual trituration preferentially destroys large, fragile neuronal nuclei while preserving smaller microglial nuclei. Compare your cell-type proportions against published spatial transcriptomics references for the same brain region and disease stage. If the spatial data shows neurons that your sequencing data lacks, the extraction method is the likely cause. The Singulator 200+ preserves neuronal nuclei through controlled mechanical processing that avoids the shear forces of manual pipetting.
Problem: DV200 values differ widely across blocks in the same longitudinal cohort
Solution: Variable DV200 within a cohort typically reflects differences in fixation conditions rather than disease stage. Brain banks that collected tissue over decades may have changed fixation protocols, or individual cases may have experienced different postmortem intervals before fixation. Group your samples by DV200 range and consider using different analytical approaches for different quality tiers: Flex for blocks above 30 percent DV200, spatial platforms for blocks below 30 percent. The S200+ recovers nuclei consistently regardless of RNA quality -- the nuclei yield is independent of the DV200 score.
Problem: Batch effects between consortium sites persist despite using the same manual protocol
Solution: "The same protocol" applied manually at different sites is not actually the same protocol. Deparaffinization timing, trituration intensity, and enzymatic incubation temperature vary by operator even when following identical written instructions. The S200+ eliminates this by automating the entire workflow with 4 pipetting steps and less than 5 minutes hands-on time. The instrument applies identical conditions at every site, removing operator interpretation from the equation. Share the replicate consistency data (1.0M/1.0M versus 1.5M/0.4M) with consortium coordinators when proposing standardization.
Problem: Brain tissue block from a 25-year-old Parkinson's cohort yields low nuclei count
Solution: Very old blocks can yield fewer nuclei due to progressive cross-linking and tissue desiccation over decades of storage. First, verify the tissue mass meets the 2 mg minimum. If the block has been heavily sectioned over the years, less tissue may remain than expected. For blocks with reduced yield, even 200,000 to 500,000 nuclei can support a 10x Flex experiment -- the loading requirement is 10,000 to 20,000 nuclei, so reduced yields are often still sufficient. If yield is genuinely low and additional sections are available, process a second section and pool the nuclei suspensions.
The precious sample problem in neuroscience FFPE
Postmortem brain tissue is singular in science: you cannot go back for more. Read each challenge below to see how the Singulator 200+ addresses it.
Irreplaceable tissue loss during processing
The problem
50-60% of precious brain tissue lost in manual processingManual FFPE protocols destroy more than half the starting material. Of what remains, only about a third are intact nuclei. For a 35-micrometer section from a twenty-year Alzheimer's cohort, most of the tissue becomes waste before data collection begins.
Lost tissue means lost decades of clinical data that cannot be re-collected from that patient.
The solution
Gentle cartridge-based processing from inputs as small as 2 mg
The Singulator 200+ uses controlled mechanical and enzymatic processing within sealed cartridges. Built-in filters reduce myelin and lipid debris. A single 50-micrometer curl consistently yields over 1 million nuclei.
>1M nuclei per curl
From a single 50-micrometer FFPE section
Operator variability and batch effect
The problem
Results change depending on who runs the protocolDeparaffinization timing drifts from 20 minutes to 12 hours when someone forgets. Trituration pressure varies between technicians. Rehydration sits overnight because it was 5 PM. These variables embed batch effects that no computational correction can fully remove.
Multi-site consortia and longitudinal studies become unreliable when the protocol changes with the operator.
The solution
Automated processing with identical conditions every run
Every sample receives identical mechanical force, timing, and enzymatic conditions within the sealed cartridge system. Less than 5 minutes of hands-on time and 4 pipetting steps mean there is almost nothing left for human variability to affect.
1.0M / 1.0M replicate yields
vs. 1.5M / 0.4M from semi-automated methods
Cell-type bias toward robust immune populations
The problem
Manual methods destroy fragile cells and skew your dataHarsh trituration destroys fragile neuronal nuclei while robust immune cells survive. The result is a dataset skewed toward microglia and other resilient populations rather than the neurons and glial subtypes that tell the biological story.
You see the cells tough enough to survive your prep, not the cells driving the disease.
The solution
Preserved cell-type diversity that reflects actual tissue biology
Controlled mechanical processing preserves fragile neuronal nuclei, cancer cells, and stromal populations. In comparative studies, the Singulator enriched for fragile cell types (ductal cancer cells, CAFs) while semi-automated methods skewed toward neutrophils.
1% erythrocyte contamination
vs. 5% from semi-automated methods
Toxic solvents and fume hood requirement
The problem
Hours in a chemical hood with xylene and CitriSolvManual FFPE deparaffinization requires 3-5 hours of labor with toxic solvents in a fume hood. Not every academic neuroscience lab has convenient fume hood access, and the solvents themselves are a health hazard for the technicians running the protocol.
Fume hood bottlenecks limit when and where FFPE processing can happen in your department.
The solution
Proprietary safe solvent, no fume hood needed
The GREEN cartridge uses a proprietary safe solvent for deparaffinization entirely within the sealed cartridge. No xylene. No CitriSolv. Any bench in any lab becomes a processing station. The entire workflow runs in about 60 minutes total.
81% reduction in hands-on time
86% fewer pipetting steps (4 vs. 28)