
| Protocol                                                                                                                                                                                                                                                                                                                            | HT  | HT with CRISPR Screening | HT with Cell Surface Protein | HT with Cell Multiplexing | HT with CRISPR Screening & Cell Multiplexing | HT with Cell Surface Protein & Cell Multiplexing |
| ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --- | ------------------------ | ---------------------------- | ------------------------- | -------------------------------------------- | ------------------------------------------------ |
| [Single Cell Protocols - Cell Preparation Guide](https://support.10xgenomics.com/single-cell-gene-expression/sample-prep/doc/demonstrated-protocol-single-cell-protocols-cell-preparation-guide)                                                                                                                                    | ✓   | ✓                        | ✓                            | ✓                         | ✓                                            | ✓                                                |
| [Methanol Fixation of Cells for Single Cell RNA Sequencing](https://support.10xgenomics.com/single-cell-gene-expression/sample-prep/doc/demonstrated-protocol-methanol-fixation-of-cells-for-single-cell-rna-sequencing)                                                                                                            | -   | ✘                        | ✘                            | ✘                         | ✘                                            | ✘                                                |
| [Isolation of Nuclei for Single Cell RNA Sequencing & Tissues for Single Cell RNA Sequencing](https://support.10xgenomics.com/single-cell-gene-expression/sample-prep/doc/demonstrated-protocol-isolation-of-nuclei-for-single-cell-rna-sequencing-and-tissues-for-single-cell-rna-sequencing)                                      | ✓\* | ✘                        | ✘                            | ✓                         | ✘                                            | ✘                                                |
| [Enrichment of CD3+ T Cells from Dissociated Tissues for Single Cell RNA Sequencing and Immune Repertoire Profiling](https://support.10xgenomics.com/single-cell-gene-expression/index/doc/demonstrated-protocol-enrichment-of-cd3-t-cells-from-dissociated-tissues-for-single-cell-rna-sequencing-and-immune-repertoire-profiling) | ✓\* | -                        | ✓\*                          | ✓\*                       | -                                            | ✓\*                                              |
| [Tumor Dissociation for Single Cell RNA Sequencing](https://support.10xgenomics.com/single-cell-gene-expression/sample-prep/doc/demonstrated-protocol-tumor-dissociation-for-single-cell-rna-sequencing)                                                                                                                            | ✓   | -                        | ✓                            | ✓                         | -                                            | ✓                                                |
| [Single Cell Suspensions from Cultured Cell Lines for Single Cell RNA Sequencing](https://support.10xgenomics.com/single-cell-gene-expression/index/doc/demonstrated-protocol-single-cell-suspensions-from-cultured-cell-lines-for-single-cell-rna-sequencing)                                                                      | ✓   | ✓                        | ✓                            | ✓                         | ✓                                            | ✓                                                |
| [Removal of Dead Cells from Single Cell Suspensions for Single Cell RNA Sequencing](https://support.10xgenomics.com/single-cell-gene-expression/sample-prep/doc/demonstrated-protocol-removal-of-dead-cells-from-single-cell-suspensions-for-single-cell-rna-sequencing)                                                            | ✓\* | ✓\*                      | ✓\*                          | ✓\*                       | ✓                                            | ✓\*                                              |
| [Moss Protoplast Suspension for Single Cell RNA Sequencing](https://support.10xgenomics.com/single-cell-gene-expression/index/doc/demonstrated-protocol-moss-protoplast-suspension-for-single-cell-rna-sequencing)                                                                                                                  | -   | -                        | -                            | -                         | -                                            | -                                                |
| [Fresh Frozen Human-Mouse Cell Line Mixtures for Single Cell RNA Sequencing](https://support.10xgenomics.com/single-cell-gene-expression/index/doc/demonstrated-protocol-fresh-frozen-human-mouse-cell-line-mixtures-for-single-cell-rna-sequencing)                                                                                | ✓   | ✓                        | ✓                            | ✓                         | ✓                                            | ✓                                                |
| [Fresh Frozen Human Peripheral Blood Mononuclear Cells for Single Cell RNA Sequencing](https://support.10xgenomics.com/single-cell-gene-expression/sample-prep/doc/demonstrated-protocol-fresh-frozen-human-peripheral-blood-mononuclear-cells-for-single-cell-rna-sequencing)                                                      | ✓   | -                        | ✓                            | ✓                         | -                                            | ✓                                                |
| [Dissociation of Mouse Embryonic Neural Tissue for Single Cell RNA Sequencing](https://support.10xgenomics.com/single-cell-gene-expression/sample-prep/doc/demonstrated-protocol-dissociation-of-mouse-embryonic-neural-tissue-for-single-cell-rna-sequencing)                                                                      | ✓   | -                        | ✓                            | ✓                         | -                                            | ✓                                                |
| [Cell Surface Protein Labeling for Single Cell RNA Sequencing Protocols](https://support.10xgenomics.com/single-cell-gene-expression/sample-prep/doc/demonstrated-protocol-cell-surface-protein-labeling-for-single-cell-rna-sequencing-protocols)                                                                                  | ✓   | -                        | ✓                            | -                         | -                                            | ✓                                                |
| [Thawing Dissociated Tumor Cells for Single Cell RNA Sequencing](https://support.10xgenomics.com/single-cell-gene-expression/sample-prep/doc/demonstrated-protocol-thawing-dissociated-tumor-cells-for-single-cell-rna-sequencing)                                                                                                  | ✓\* | ✓\*                      | ✓\*                          | ✓\*                       | ✓\*                                          | ✓\*                                              |
| [Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocols](https://support.10xgenomics.com/single-cell-gene-expression/index/doc/demonstrated-protocol-cell-multiplexing-oligo-labeling-for-single-cell-rna-sequencing-protocols)                                                                                  | -   | -                        | -                            | ✓                         | ✓                                            | ✓                                                |
| [High Throughput Sample Preparation for Single Cell RNA Sequencing](https://support.10xgenomics.com/single-cell-gene-expression/overview/doc/demonstrated-protocol-high-throughput-sample-preparation-for-single-cell-rna-sequencing)                                                                                               | -   | -                        | -                            | ✓                         | -                                            | -                                                |

✓ Compatible (tested in-house)
✓\* Untested but low risk
\*\* Compatible but unsupported
\- Untested, use at your own risk
✘ Incompatible


Lists compatibility of single cell sample preparation Demonstrated Protocols with downstream Chromium Single Cell HT (high-throughput) assays.

Single Cell Gene Expression HT Demonstrated Protocol Compatibility Table

Prepare optimal single cell/nuclei suspension by following our Demonstrated Protocols.

Sample Prep

Chromium Single Cell Gene Expression provides single cell transcriptome 3' gene expression alongside the detection of surface protein expression or CRISPR edits in tens of thousands of cells. Scale experiments up or down with low-throughput and high-throughput solutions.

Plan ahead by referring to the list of equipment, kits, and reagents needed for Single Cell Gene Expression.

Experimental Design

Experimental Design & Planning

Refer to instrument-specific documents for seamless instrument operation.

Instruments

Construct a sequencing-ready single cell library by following our step-by-step User Guide / Protocol.

Library Construction

Use pre-designed or custom panels for targeted gene expression, followed by sequencing and data analysis.

Targeted

Targeted Gene Expression (Optional)

Sequence your single cell library as per our provided recommendations.

Sequencing

Analyze your single cell data using our pipelines, visualization, and Cloud Analysis tools.

Software Analysis

Chromium X Series

Single Cell Gene Expression

Overview

Documentation

Additional Applications

Datasets

Videos

Publications

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Chromium Single Cell Gene Expression provides single cell transcriptome 3' gene expression alongside the detection of surface protein expression in tens of thousands of cells.

What is Single Cell Gene Expression?

Measure single cell gene and cell surface protein expression simultaneously.

Cell Surface Protein

Assess effects of CRISPR perturbations alongside single cell gene expression.

CRISPR

Multiplex up to 12 samples per channel for increased sample throughput.

Cell Multiplexing

Profile 2,000–20,000 cells per channel of the Chromium Next GEM Chip M (2,000– 60,000 cells per channel with CellPlex).

High Throughput (HT)

We provide resources from protocols, user guides, and free-to-use analysis tools.

Access free, publicly available data from a number of different sample types generated with Chromium single cell solutions.

Explore how-to videos and training modules.

Chromium Next GEM Single Cell 3' v3.1 - Dual Index

Chromium Next GEM Single Cell 3' v3.1 - Single Index

Chromium Next GEM Single Cell 3' HT v3.1 - Dual Index

Find answers to common technical questions, from sample prep through data analysis, about Chromium single cell workflows.

Read key peer-reviewed research publications offering greater insights into biology, enabled by 10x Genomics products and technologies.