Single Cell Sequencing Services

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Achieve a more nuanced view of biology

While extracting and sequencing nucleic acid from bulk tissue can provide a great deal of information, understanding the status of individual cells is often critical for truly understanding normal and aberrant physiology.

HudsonAlpha Discovery supports single cell genomic studies by combining our optimized processes and protocols with technologies from 10x Genomics. We offer RNA-Seq for understanding the transcriptome, CITE-seq to simultaneously assess surface proteins and the transcriptome, and ATAC-seq to explore chromatin accessibility.


Improve the resolution of your genomic data with single cell sequencing services.

10x Genomics technologies

Single cell RNA-Seq service

Multidimensional multi-omics data with CITE-seq

Chromatin accessibility with ATAC-seq

V(D)J B cell receptor and T cell receptor sequencing

Qualitative and quantitative analyses


  • Immune repertoire profiling
  • Transcriptomics
  • Biomarker discovery & profiling
  • Quantitative analysis
  • Personalized medicine
  • All research phases and activities
    • Basic discovery
    • Translational and pre-clinical
    • Clinical

Highlights of our single cell sequencing services

Enhance your understanding of biology through single cell genomics and multi-omics data:
Multiple types of assays
  • RNA-Seq for mRNA
  • CITE-seq for simultaneous mRNA and surface protein
  • ATAC-seq for chromatin accessibility
  • V(D)J B cell receptor (BCR) sequencing and T cell receptor (TCR) sequencing
  • Combined total RNA-Seq with V(D)J BCR sequencing and V(D)J TCR sequencing
Nucleic acid extraction and library preparation
  • Optimized extraction protocols for nearly any sample type
  • Optimized protocols for working with ultra-low amounts of nucleic acid
  • Dual concurrent RNA-DNA extraction from challenging sample types such as FFPE tissue— read the white paper »
Bioinformatics analysis and data storage
  • Tier 1: Raw BCL and FASTQ file output
  • Tier 2: Standard application-specific and quality report outputs (BCL, FASTQ, aligned BAM files and sequencing QC reports
  • Tier 3: Standard output plus variant calling (VCF, g-VCF) and genomic interpretation reports
  • Additional custom reporting options including Ingenuity Variant Analysis (Qiagen) consolidated variant reports as well as options for genomic variant annotation
  • Flexible data delivery and storage options
  • 90 days storage included with service pricing
  • Long term storage available

The HudsonAlpha Discovery Difference

Single cell sequencing services
Flexible and creative problem solving with expert scientific guidance
Optimized protocols and automated workflows that reduce technical bias
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Stringent quality control parameters—we consistently exceed manufacturer specifications—for reproducible, accurate results
Services that streamline analysis of fresh and frozen cells and tissues thanks to the close proximity of cell biology, cell dissociation, flow cytometry, and genomic labs
Massive scale with 10 Illumina NovaSeq 6000 sequencers as well as NextSeqs, MiSeqs, and iSeqs
A decade of proven experience spanning thousands of projects and hundreds of publications
See Recent Publications
Recent Publications
  1. 10x Genomics. Demonstrated Protocol: Removal of Dead Cells for Single Cell RNA Sequencing. CG000093-Rev C. 2020.
  2. 10x Genomics. Thawing Dissociated Tumor Cells for Single Cell RNA Sequencing. CG000233-Rev A. 2019.

Get more information about our DNA and RNA sequencing services

Download the One-Sheet

Propel Your Research

Leverage the power of the HudsonAlpha Discovery division; contact us today!