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Single-Cell Sequencing Reagents:

A Complete Workflow Guide with Ready-to-Source Kits from Avantor

 Single-Cell Sequencing Reagents & Workflow Guide | Avantor

Single-cell sequencing

Single-cell sequencing is transforming life sciences by unlocking cell-by-cell insights previously hidden in bulk population averages. Whether you're uncovering immune cell diversity, profiling tumor heterogeneity, or building multi-omic atlases of complex tissues, the ability to analyze individual cells has become a foundational tool in research and translational medicine.

But running a successful single-cell experiment requires more than just instrumentation — it demands precision at every step, and that means sourcing the right reagents, kits, and consumables specifically optimized for low-input workflows.

This guide walks through a full single-cell RNA-seq (scRNA-seq) workflow and links each step with curated Avantor products you can source directly to build or enhance your single-cell pipeline.

Step 1: Sample Preparation – High Viability, Single-Cell Suspensions
Single-cell experiments succeed or fail at the sample prep stage. Generating a debris-free, high-viability suspension of individual cells is the foundation of everything that follows.

Recommended Products
 
Product Description Link
Accumax™ Cell Dissociation Solution Enzyme-free reagent for gentle tissue dissociation View Product
Collagenase Protease blend for effective dissociation of collagen-rich tissues View Product
Corning® Dispase Gentle enzyme for detaching cells from Matrigel and ECM matrices View Product
MTT Viability Assay Metabolic activity stain to confirm sample viability View Product
Step 2: Single-Cell Capture – Partitioning Cells for Barcoding

Once a single-cell suspension is achieved, the next step is to isolate each cell for individual processing — commonly via droplets, nanowells, or FACS.                                   

Recommended Products

Product Description Link
Stilla® Sapphire Chip Microfluidic chip for droplet-based workflows View Product
Stilla® Ruby Chip High-throughput droplet chip with automation compatibility View Product
FACS & IF Staining Buffer – BSA Optimized for sorting sensitive cell types View Product
FACS & IF Staining Buffer – FBS or Goat Serum Prevents background staining and maintains cell health during sorting View FBS / View Goat Serum
Step 3: Reverse Transcription & Barcoding – Capturing the Transcriptome
Once cells are isolated, RNA must be captured and converted to cDNA — with unique barcodes and molecular identifiers (UMIs) that preserve cell-level resolution.       

Recommended Products
Product Description Link
Template Switching RT Enzyme Mix Enables full-length cDNA synthesis via template-switching View Product
NEBNext® Single Cell/Low Input RNA Kit End-to-end kit for single-cell barcoding and cDNA generation View Product
NEBNext® Cell Lysis Module Protects RNA during lysis in low-input workflows View Product
Step 4: cDNA Amplification – Boosting Signal Without Bias
Since each cell yields only picograms of cDNA, sensitive amplification is essential before library preparation.

While no direct products were returned in the API, Avantor stocks:
  • High-fidelity PCR kits for low-input workflows (search: "high-fidelity PCR enzyme")
  • Whole Transcriptome Amplification (WTA) kits (search: "WTA kit")
  • Magnetic bead-based PCR cleanup (search: "AMPure XP alternative")

 Search PCR & Cleanup Kits 

Step 5: Library Preparation – Adapters, Indices & Tagmentation
Preparing your cDNA for sequencing involves attaching platform-specific adapters, purifying libraries, and pooling indexed samples.                                                                        

Recommended Products
Product Description Link
sparQ UDI Adapters (1–96) Dual-indexed adapters for multiplexed sequencing View Product
NEBNext® Ultra II RNA Library Prep Kit Standard library prep for RNA-seq from low-input material View Product
NEBNext® Ultra II Directional Kit Strand-specific RNA-seq for single-cell workflows View Product
Zymo-Seq™ ATAC Library Kit For open chromatin profiling and multi-omic workflows View Product
Step 6: Sequencing & Quality Control – From Library to Data
Before sequencing, libraries must be quantified and checked for size distribution. Then, they’re ready for loading on Illumina flow cells or other sequencing platforms.

 No products were returned via API, but you can easily find or request: 
Product Action
Qubit™ dsDNA HS Assay KitSearch on Avantor
Bioanalyzer HS DNA KitSearch on Avantor
Illumina Sequencing Reagents & Flow CellsContact Avantor for Support
NGS-grade plastics, tubes, capsSearch: NGS Consumables

Why Avantor is Your Trusted Partner for Single-Cell Reagents

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Avantor provides:

  • End-to-end reagent support for single-cell workflows
  • Cold-chain logistics for sensitive enzymes
  • Regulatory-grade documentation for clinical/GLP labs
  • Procurement simplification across thousands of SKUs
  • Personalized support for platform compatibility and custom orders

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Ready to Build Your Single-Cell Pipeline?

Explore Avantor’s full range of single-cell and RNA-seq products online or speak with a technical representative to get help configuring the right kits for your platform.

Start Browsing Single-Cell Reagents

Avantor — Empowering Single-Cell Innovation, One Kit at a Time. 

Contact an Avantor Specialist