- [Resource Hub](/) - FFPE Resources # FFPE Resources 36 resources ## All Resources Filters Clear All Resource Type Field Guide Ebook Webinar Protocol Blog Post Publication Brochure Application Note Customer Published Protocol Instrument Singulator 200+ Singulator 100 Singulator 200 Application FFPE Tissue Neuroscience Single Cell Genomics Tissue Dissociation Cardiovascular Developmental Biology Immunology Oncology Organoid Drug Discovery Tissue Type Brain/CNS Breast Cancer Cardiovascular/Heart Cartilage Cervix Colon Embryo Esophagus Fallopian Tube Intestine Kidney Leaves Liver Lung Lymph Node Meniscus Nasal Mucosa Ovary Pancreas Peripheral Blood Lymphocytes Placenta Prostate Salivary Gland Skeletal Muscle Skin Spleen Synovium & Infrapatellar Fat Pad Testes Thalamus Thymus Uterus Downstream Application 10x Chromium Flex Cell or Nuclei Nuclei Showing 36 of 36 resources Filters [Field Guide](/resources/brain-tissue-complexity-myelin-lipids-neuronal-nuclei/) Singulator 200+ ### Overcoming Brain Tissue Complexity: Myelin, Lipids, and Fragile Neuronal Nuclei Brain FFPE tissue creates unique nuclei isolation challenges. Myelin debris, lipid contamination, and fragile neuronal nuclei require controlled automated processing to preserve cell-type diversity for single-nucleus sequencing. [Read Field Guide](/resources/brain-tissue-complexity-myelin-lipids-neuronal-nuclei/) [Field Guide](/resources/brain-tumor-ffpe-surgical-resection-single-cell/) Singulator 200+ ### Brain Tumor FFPE Processing: From Surgical Resection to Single-Nucleus Insights Process brain tumor FFPE from surgical resections on the Singulator 200+. Preserve cancer cells and immune populations for snRNA-seq and spatial analysis. [Read Field Guide](/resources/brain-tumor-ffpe-surgical-resection-single-cell/) [Ebook](/resources/cold-case-files-neuroscience-ffpe/) Singulator 200+ ### Cold Case Files:The Brain's Embedded Evidence How the Singulator 200+ preserves fragile neuronal nuclei from irreplaceable postmortem brain tissue. Automated FFPE processing for Alzheimer's, brain tumors, and brain atlases. [Read Ebook](/resources/cold-case-files-neuroscience-ffpe/) [Field Guide](/resources/ffpe-neurodegenerative-disease-research-singulator/) Singulator 200+ ### FFPE Nuclei Extraction for Neurodegenerative Disease Research Extract nuclei from FFPE brain tissue for Alzheimer's, Parkinson's, and Lewy body research. Longitudinal cohorts, cell-type preservation, and disease staging on the Singulator 200+. [Read Field Guide](/resources/ffpe-neurodegenerative-disease-research-singulator/) [Field Guide](/resources/integrating-snrna-seq-spatial-transcriptomics-brain-ffpe/) Singulator 200+ ### Integrating snRNA-seq with spatial transcriptomics for brain mapping Pair spatial transcriptomics with snRNA-seq from the same FFPE brain block. Block allocation, platform selection, and nuclei quality for multi-omic brain studies. [Read Field Guide](/resources/integrating-snrna-seq-spatial-transcriptomics-brain-ffpe/) [Field Guide](/resources/maximizing-limited-brain-tissue-sections-ffpe/) Singulator 200+ ### Maximizing Results from Limited Brain Tissue Sections Get high-quality nuclei from limited postmortem brain FFPE sections. Process NIH biobank allocations, hospital archives, and surgical specimens on the Singulator 200+. [Read Field Guide](/resources/maximizing-limited-brain-tissue-sections-ffpe/) [Field Guide](/resources/navigating-postmortem-brain-tissue-ffpe-genomics/) Singulator 200+ ### Navigating postmortem brain tissue for FFPE genomics Practical guide to postmortem brain FFPE challenges: necropsy timing, fixation variability, biobank sourcing, myelin debris, and how the Singulator 200+ standardizes nuclei extraction. [Read Field Guide](/resources/navigating-postmortem-brain-tissue-ffpe-genomics/) [Field Guide](/resources/reproducible-multi-site-brain-tissue-atlases-singulator/) Singulator 200+ ### Building Reproducible Multi-Site Brain Tissue Atlases Standardize brain FFPE nuclei extraction across consortium sites with the Singulator 200+. Eliminate operator variability, prevent batch effects, and scale for atlas projects. [Read Field Guide](/resources/reproducible-multi-site-brain-tissue-atlases-singulator/) [Webinar](/resources/unlocking-single-cell-insights-from-ffpe-samples/) Singulator 200+ ### Unlocking Single-Cell Insights from FFPE Samples Ronan Chaugnet from Memorial Sloan Kettering shares several years of head-to-head benchmarking data comparing nuclei extraction platforms for FFPE tissue. The Singulator 200+ and Miltenyi GentleMACS both outperformed manual approaches across glioblastoma, liver, lung, pancreas, and tumor samples, with the Singulator 200+ standing out for its fully automated, enzyme-free workflow. Ronan also walks through three methods his lab has built on top of automated FFPE extraction: 10X Genomics FLEX for high-quality gene expression, PERFF-Seq for sorting rare cell populations by RNA markers, and GIFT-Seq for detecting 600+ mutations at single-cell resolution from archival tissue. [Read More](/resources/unlocking-single-cell-insights-from-ffpe-samples/) [Protocol](https://precisioncellsystems.com/wp-content/uploads/2026/03/Automating-Nuclei-Isolation-from-FFPE-Tissues-for-Single-Nuclei-Sequencing-Applications.pdf) Singulator 200+ ### Automating Nuclei Isolation from FFPE Tissues for Single-Nuclei Sequencing Applications This protocol describes how to isolate, count, and prepare single nuclei from FFPE (formalin-fixed, paraffin-embedded) tissues for single-nuclei sequencing assays using the Singulator 200+ platform. Deparaffinization and rehydration of the tissue using solvent and various concentrations of ethanol are conducted on the Singulator 200+ platform along with automated nuclei isolation. [Read Protocol](https://precisioncellsystems.com/wp-content/uploads/2026/03/Automating-Nuclei-Isolation-from-FFPE-Tissues-for-Single-Nuclei-Sequencing-Applications.pdf) [Blog Part 5](/resources/cold-case-closed-brain-atlas/) Singulator 200+ ### Cold Case - Part 5: Case Closed Brain atlases are being built. Archival tissue is finally talking. How standardized nuclei extraction and platform-agnostic analysis are solving neuroscience's oldest cold cases. [Read Blog](/resources/cold-case-closed-brain-atlas/) [Blog Part 2](/resources/cold-case-contaminated-evidence-brain-tissue/) Singulator 200+ ### Cold Case - Part 2: Contaminated Evidence Manual extraction of nuclei from FFPE brain tissue destroys 50 to 60 percent of starting material. Fragile neurons die first, leaving biased results. Here is what goes wrong. [Read Blog](/resources/cold-case-contaminated-evidence-brain-tissue/) [Blog Part 1](/resources/cold-case-files-brain-tissue-evidence/) Singulator 200+ ### Cold Case - Part 1: The Cold Case Files Millions of FFPE brain tissue blocks sit in biobanks worldwide, holding decades of evidence about Alzheimer's, Parkinson's, and neurodegenerative diseases. What if we could reopen these cases? [Read Blog](/resources/cold-case-files-brain-tissue-evidence/) [Blog Part 4](/resources/cold-case-forensic-lab-singulator-200-plus/) Singulator 200+ ### Cold Case - Part 4: The Forensic Lab Manual FFPE processing destroys fragile neuronal nuclei and produces variable results. The Singulator 200+ automates the workflow with a two-cartridge system that delivers consistent, operator-independent results from irreplaceable brain tissue. [Read Blog](/resources/cold-case-forensic-lab-singulator-200-plus/) [Blog Part 3](/resources/cold-case-one-shot-at-the-scene/) Singulator 200+ ### Cold Case - Part 3: One Shot at the Scene NIH biobanks give you one allocation of irreplaceable brain tissue. Manual processing destroys 50-60% before analysis begins. The extraction method is the real variable. [Read Blog](/resources/cold-case-one-shot-at-the-scene/) [Field Guide](/resources/complete-ffpe-workflow-archive-to-publication-singulator/) Singulator 200+ ### Complete FFPE workflow: from archive to publication with the Singulator 200+ End-to-end protocol walkthrough from FFPE block selection through deparaffinization, nuclei isolation, quality control, library preparation, sequencing, and data analysis using the Singulator 200+. [Read Field Guide](/resources/complete-ffpe-workflow-archive-to-publication-singulator/) [Field Guide](/resources/deparaffinization-rehydration-singulator-200-plus-green-cartridge/) Singulator 200+ ### Deparaffinization Rehydration Optimization How the Singulator 200+ GREEN cartridge automates FFPE deparaffinization and rehydration, eliminating toxic solvents, fume hoods, and manual ethanol series from nuclei extraction workflows. [Read Field Guide](/resources/deparaffinization-rehydration-singulator-200-plus-green-cartridge/) [Field Guide](/resources/ffpe-downstream-platform-compatibility/) Singulator 200+ ### FFPE Downstream Platform Compatibility Practical guide to connecting Singulator 200+ FFPE nuclei with downstream analysis platforms including 10x Chromium Flex, Xenium, ATAC-seq, Visium, and MERFISH, covering quality requirements, expected yields, and multi-platform study design. [Read Field Guide](/resources/ffpe-downstream-platform-compatibility/) [Field Guide](/resources/ffpe-input-preparation-optimizing-curl-thickness-tissue-mass-block-age-singulator-200-plus/) Singulator 200+ ### FFPE Input Preparation Practical guide to preparing FFPE tissue inputs for the Singulator 200+ automated nuclei extraction platform, covering curl thickness selection, tissue mass requirements, block age effects, quality assessment, and handling difficult or precious specimens. [Read Field Guide](/resources/ffpe-input-preparation-optimizing-curl-thickness-tissue-mass-block-age-singulator-200-plus/) [Field Guide](/resources/ffpe-troubleshooting-guide-singulator-200-plus/) Singulator 200+ ### FFPE Troubleshooting Guide: Diagnosing and Resolving Common Singulator 200+ Issues Practical troubleshooting guide for the Singulator 200+ FFPE nuclei extraction workflow, covering the five most common problem categories: low yield, excessive debris, poor RNA quality, batch-to-batch variability, and cartridge/instrument errors. [Read Field Guide](/resources/ffpe-troubleshooting-guide-singulator-200-plus/) [Field Guide](/resources/minimal-precious-ffpe-samples-singulator-200-plus/) Singulator 200+ ### Working with Minimal and Precious FFPE Samples Practical strategies for maximizing nuclei recovery from limited FFPE tissue on the Singulator 200+, covering block quality assessment, sectioning waste reduction, the pilot curl approach for irreplaceable specimens, handling needle biopsies and crumbly blocks, and preserving nuclei yield post-processing. [Read Field Guide](/resources/minimal-precious-ffpe-samples-singulator-200-plus/) [Field Guide](/resources/nuclei-isolation-quality-assessment-yield-viability-dv200-ffpe-singulator/) Singulator 200+ ### FFPE Nuclei Isolation Quality Assessment Quality assessment of nuclei isolated from FFPE tissue using the Singulator 200+, covering yield measurement, DAPI staining for morphology, DV200 RNA quality metrics, erythrocyte contamination assessment, and structured go/no-go decision frameworks before downstream sequencing. [Read Field Guide](/resources/nuclei-isolation-quality-assessment-yield-viability-dv200-ffpe-singulator/) [Ebook](/resources/tissue-dissociation-protocol-guide/) Singulator 100 Singulator 200 Singulator 200+ ### Tissue Dissociation Guide The most comprehensive tissue dissociation reference available. Interactive protocols for single-cell isolation and nuclei extraction across 57+ tissue types with community and Singulator-optimized methods. [Read Ebook](/resources/tissue-dissociation-protocol-guide/) [Ebook](/resources/unlock-the-archive-ffpe-nuclei-extraction/) Singulator 200+ ### Unlock the Archive: Automated FFPE Nuclei Extraction for Single-Cell Genomics How formalin-fixed paraffin-embedded tissue archives hold enormous potential for single-cell genomics, and how the Singulator 200+ automates the nuclei extraction workflow to unlock that potential [Read Ebook](/resources/unlock-the-archive-ffpe-nuclei-extraction/) [Blog Part 1](/resources/unlocking-ffpe-archives-part-1-the-ffpe-fortune/) Singulator 200+ ### Unlocking FFPE Archives - Part 1: The FFPE Fortune - What's Hidden in Your Biobank? Somewhere in your institution, there's a dusty shelf. Sitting on it: thousands of tissue blocks. Each one holds decades of clinical history. Patient outcomes. Treatment responses. Disease progression. Data that took years to collect. And can you blame researchers for walking past it? [Read Blog](/resources/unlocking-ffpe-archives-part-1-the-ffpe-fortune/) [Blog Part 2](/resources/unlocking-ffpe-archives-part-2-ffpe-chemistry-problem-preservation-prison/) Singulator 200+ ### Unlocking FFPE Archives - Part 2: The Chemistry Problem: Why Preservation Became a Prison Here's a weird fact: the same chemical that saves your sample also traps everything useful inside it. Think about laminating a document. Great for protection. Terrible if you need to edit what's inside. That's formalin. And for decades, nobody could undo the damage. [Read Blog](/resources/unlocking-ffpe-archives-part-2-ffpe-chemistry-problem-preservation-prison/) [Blog Part 3](/resources/unlocking-ffpe-archives-part-3-manual-vs-modern-workflow-debate/) Singulator 200+ ### Unlocking FFPE Archives - Part 3: Manual Methods vs. Modern Science: The Great Workflow Debate Third try. Third failure. The fume hood is running. The xylene smells terrible. And the protocol that worked last Tuesday is giving nothing but debris. Sound familiar? Here's the question nobody was asking: Is it your technique—or is it the physics? [Read Blog](/resources/unlocking-ffpe-archives-part-3-manual-vs-modern-workflow-debate/) [Blog Part 4](/resources/unlocking-ffpe-archives-part-4-two-hours-sixty-minutes-automation/) Singulator 200+ ### Unlocking FFPE Archives - Part 4: From Two Hours to Sixty Minutes: What Automation Actually Changes What if that two-hour protocol took sixty minutes? What if twelve pipetting steps dropped to four? What if the fume hood became optional? These aren't hypotheticals. This is what purpose-built automation looks like. And the difference isn't just time. [Read Blog](/resources/unlocking-ffpe-archives-part-4-two-hours-sixty-minutes-automation/) [Blog Part 5](/resources/unlocking-ffpe-archives-part-5-the-archive-opens-are-you-ready/) Singulator 200+ ### Unlocking FFPE Archives - Part 5: The Archive Opens: Are You Ready? Behind every tissue block is a patient who said yes. Yes to collection. Yes to research. Yes to the hope that their gift might help someone else. They trusted the science. The question now: are the protocols worthy of that trust? [Read Blog](/resources/unlocking-ffpe-archives-part-5-the-archive-opens-are-you-ready/) [Publication](https://pmc.ncbi.nlm.nih.gov/articles/PMC12259082/) Singulator 200+ ### Oncogenic and tumor-suppressive forces converge on a progenitor-orchestrated niche to shape early tumorigenesis [View Publication](https://pmc.ncbi.nlm.nih.gov/articles/PMC12259082/) [Brochure](https://precisioncellsystems.com/wp-content/uploads/2025/12/S200_Brochure_final_v1.pdf) Singulator 200+ ### Brochure - Singulator 200+ [Download Brochure](https://precisioncellsystems.com/wp-content/uploads/2025/12/S200_Brochure_final_v1.pdf) [Brochure](https://precisioncellsystems.com/wp-content/uploads/2025/12/S200_Brochure_FFPE_final_v1.pdf) Singulator 200+ ### Brochure - S200+ - FFPE [Download Brochure](https://precisioncellsystems.com/wp-content/uploads/2025/12/S200_Brochure_FFPE_final_v1.pdf) [App Note](https://precisioncellsystems.com/wp-content/uploads/2025/11/Applicaiton_Note_Singulator_FFPE_v1_11-30-25.pdf) Singulator 200+ ### FFPE Tissue Dissociation [Download App Note](https://precisioncellsystems.com/wp-content/uploads/2025/11/Applicaiton_Note_Singulator_FFPE_v1_11-30-25.pdf) [Protocol](https://www.protocols.io/view/1-perff-seq-cell-and-nuclei-preparation-c8n3zvgn.html?__hstc=225964101.fe4380f775ce29a6a07134828a8c07b8.1742318073258.1743114390284.1743120525713.7&__hssc=225964101.3.1743120525713&__hsfp=1300058700&submissionGuid=cb652c05-65bb-4462-94bc-f6d6270950ee) Singulator 200+ ### PERFF-seq: Cell and Nuclei Preparation [Read Protocol](https://www.protocols.io/view/1-perff-seq-cell-and-nuclei-preparation-c8n3zvgn.html?__hstc=225964101.fe4380f775ce29a6a07134828a8c07b8.1742318073258.1743114390284.1743120525713.7&__hssc=225964101.3.1743120525713&__hsfp=1300058700&submissionGuid=cb652c05-65bb-4462-94bc-f6d6270950ee) [Publication](https://pmc.ncbi.nlm.nih.gov/articles/PMC12276987/) Singulator 200+ ### Transcript-specific enrichment enables profiling rare cell states via scRNA-seq [View Publication](https://pmc.ncbi.nlm.nih.gov/articles/PMC12276987/) [Publication](https://www.nature.com/articles/s41587-024-02193-4?__hstc=225964101.fe4380f775ce29a6a07134828a8c07b8.1742318073258.1743189924157.1743558253016.10&__hssc=225964101.24.1743558253016&__hsfp=1300058700&submissionGuid=d4eb5dac-02d7-45d8-953c-6c79fc38c05f) Singulator 200+ ### The covariance environment defines cellular niches for spatial inference [View Publication](https://www.nature.com/articles/s41587-024-02193-4?__hstc=225964101.fe4380f775ce29a6a07134828a8c07b8.1742318073258.1743189924157.1743558253016.10&__hssc=225964101.24.1743558253016&__hsfp=1300058700&submissionGuid=d4eb5dac-02d7-45d8-953c-6c79fc38c05f) No resources match your current filters. 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