Chromium Single Cell

Access the broadest range of analytes, samples & workflows

Confidently tackle any research question using the only single cell toolkit with optimized protocols and proven performance for fresh, frozen, and fixed samples—even FFPE.
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Flex Apex

Plate-based multiplexing with Apex has transformed Flex, enabling unprecedented scale. And because it’s powered by Chromium automated cell partitioning, superior performance comes standard. The benefits of plates plus Apex:

  • Profile up to 384 samples in a 96-well format

  • Run partial plates today, save the rest for later

  • Streamline sample handling with automation compatibility

Gene expression

Whole transcriptome coverage

Profile the whole transcriptome by capturing the 3’ or 5’ ends of mRNA transcripts for unbiased characterization of cell types and states from a wide range of species.

Specifications

Cell suspensions

Nuclei suspensions

Flow-sorted cells

Fixed human PBMCs

Fresh tissue

Frozen tissue

DSP/Methanol-fixed tissue

Organoids

Protein coding gene coverage

Sensitive, robust profiling of 18,000+ genes from human and mouse, even from whole tissue, FFPE samples, and samples with fragmented RNA.

Specifications

Cell suspensions

Nuclei suspensions

Flow-sorted cells

Fixed whole blood

Fresh tissue

Frozen tissue

FFPE tissue

PFA-fixed tissue

Organoids

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Chromatin accessibility

Chromatin accessibility

Analyze thousands of unique open chromatin fragments per cell, genome-wide, to gain insights into deeper understandings of the cell type–specific regulatory mechanisms.

Specifications

Nuclei suspensions

Fresh tissue

Frozen tissue

Multiomic profiling

CRISPR

Evaluate gene function across different cellular processes with direct assessment of CRISPR-driven edits or knockdowns and their resulting gene expression phenotypes.

Cell surface protein

Characterize cell subtypes and states more comprehensively with added protein information from the same cell, allowing you to explore transcriptomic and proteomic relationships.

Intracellular protein

Enrich distinct cell phenotype understanding with added protein expression data throughout the entire cell, including nuclear, cytosolic, and secreted proteins.

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T cell receptor/B cell receptor

Gain a comprehensive view of the immune system with paired, full-length receptor sequences from T and/or B cells with complete isotype resolution.

Featured resources

Antigen specificity

Obtain comprehensive antigen-specific cellular profiles to identify rare, antigen-reactive T and B cells to fully characterize the adaptive immune response and accelerate therapeutic discovery.

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Unique sample prep capabilities

Nuclei isolation from frozen samples

Easily and efficiently prepare frozen samples for single nuclei sequencing, consolidating your experimental processes and improving access to more samples.

Nuclei isolation from FFPE samples

Isolate nuclei from FFPE tissue sections for use with Apex. Now includes a scalable, faster, heat-based protocol.

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Featured resources

Whole blood fixation

Fix then isolate peripheral blood mononuclear cells (PBMCs) and leukocytes from whole blood upstream of the Apex assay, enabling more flexible and convenient blood-based studies.

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Human PBMC fixation

Fix, store, and perform 3’ or 5’ gene expression on human PBMC samples on your schedule, without sacrificing RNA integrity or fragile cell types.

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Chop/Fix

Start with whole tissue, chop it into smaller pieces, and then fix prior to dissociation into a cell suspension, preserving fragile cells that would not survive other dissociation methods.

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Additional experimental options

Long-read sequencing

Combine long-read sequencing with Chromium assays to identify alternative isoforms and splicing at single cell resolution.

Custom probe design

Target additional mRNAs of interest not covered in the standard Flex transcriptome probe sets, letting you tailor your experiments to your research needs.

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Plate-based sample handling

Run up to 384 samples or 100M cells a week with convenient 96-well multiplexing and automation compatibility

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See Chromium Single Cell’s powerful and versatile capabilities in action

Discover how researchers across the globe have used Chromium Single Cell to discover novel cell types and states, understand disease mechanisms, and beyond.

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