Single Cell Sequencing Services

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

Enhance your understanding of biology through single cell genomics and multi-omics data:

Highlights of Our Single Cell Sequencing Services

Here are a few examples of what we offer:

Multiple types of assays

  • scRNASeq 3' or 5' GEX (Gene Expression)
  • CITE-seq for simulataneous mRNA and surface protein
  • ATAC-seq for chromatin
  • 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
  • Cell Sorting
  • Single Nuclei Isolations

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

Single cell sequencing services

The HudsonAlpha Discovery Difference

Stringent quality control parameters—we consistently exceed manufacturer specifications—for reproducible, accurate results


Flexible and creative problem solving with expert scientific guidance


Optimized protocols and automated workflows that reduce technical bias


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 9 Illumina NovaSeq 6000 sequencers as well as NextSeqs, MiSeqs, and iSeqs


A decade of proven experience spanning thousands of projects and hundreds of 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.

To propel your projects with The Power of Discovery.™

Contact Us Today

Let us know about your project!