Library Preps - Single Cell

All assays include partitioning and barcoding using the Chromium Controller and manual library preparation.

Chromium Single Cell Gene Expression

  • Gene expression profiling for characterization of tens of thousands of single cells
    • Identify rare cell types
    • Atlas and characterize complex cell populations
    • Understand cellular heterogeneity
    • Discover new biomarkers
  • Input:
    • 500 - 10,000 cells or nuclei
  • Suitable for:
    • Cells or nuclei
    • Flow-sorted cells
    • Cells labeled with cell surface protein antibodies
    • Cells expressing compatible CRISPR guides
  • Molecular barcoding and capture:
    • Capture and amplify 3' mRNA
    • Capture and identify cell surface proteins and CRISPR perturbations

Chromium Single Cell Immune Profiling

  • Paired, full-length receptor sequencing and gene expression profiling for tens of thousands of T and B cells
    • Profile immune cell repertoires
    • Determine antigen specificity of B cells and T cells
    • Characterize tissue microenvironments
    • Go beyond traditional cytometry
  • Input:
    • 500 - 10,000 cells
  • Suitable for:
    • Cells
    • Flow-sorted cells
    • Cells labeled with cell surface protein antibodies
    • Cells labeled for antigen specificity analysis
  • Molecular barcoding and capture:
    • Capture and amplify 5' mRNA
    • Capture and sequence paired, full-length BCR/TCR genes
    • Capture and identify cell surface proteins and antigen-specific immune receptors

Chromium Single Cell Multiome ATAC + Gene Expression

  • Simultaneous gene expression and open chromatin profiling from the same cell for tens of thousands of cells
    • Link regulatory elements and target genes
    • Characterize cell heterogeneity
    • Discover new gene regulatory interactions
    • Identify rare cell types
  • Input:
    • 500 - 10,000 nuclei
  • Suitable for:
    • Nuclei treated with transposase
  • Molecular barcoding and capture:
    • Capture and amplify transposase-accessible DNA fragments
    • Capture and amplify 3' mRNA

Chromium Single Cell ATAC

  • Assay for transposase-accessible chromatin (ATAC) for epigenomic analysis of tens of thousands of individual nuclei
    • Define cell types and states
    • Catalog cell type–specific regulatory elements
    • Identify important transcription factors
    • Characterize gene regulatory networks
  • Input:
    • 500 - 10,000 nuclei
  • Suitable for:
    • Nuclei treated with transposase
  • Molecular barcoding and capture:
    • Capture and amplify transposase-accessible DNA fragments

Other Options

  • Requests for projects requiring significant modifications to existing protocols or library preparation options not already listed here will be discussed with the customer on a per-project basis.

Sample Submission

  • We cannot accept any samples that would be classified as Biosafety Level 2 (BSL2) or higher!
  • We work closely with the customer to coordinate sample submission and workflow timelines to optimize cell viability and recovery.
  • The maximum cell size 10x Genomics tested in-house is 30 μm. 10x Genomics did not observe differential recovery for small vs. large cells when running a sample composed of cells of different sizes (for cells that are equal to or smaller than 30 μm).
  • The recommended starting point for a new sample type is to load ~1,700 cells into each reaction, recovering approximately 1,000 cells, to achieve an expected multiplet rate of approximately 0.8%. For comparison, loading ~17,400 cells and recovering approximately 10,000 cells yields a multiplet rate of approximately 7.6%.

Notes & Resources