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Single Cell Gene Expression

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What is Single Cell Gene Expression?

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.

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Documentation

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

Experimental Design & Planning

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

Sample Prep

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

Instruments

Refer to instrument-specific documents for seamless instrument operation.

Library Construction

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

Targeted Gene Expression (Optional)

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

Sequencing

Sequence your single cell library as per our provided recommendations.

Software Analysis

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

Additional Applications

Cell Surface Protein
Measure single cell gene and cell surface protein expression simultaneously.
CRISPR
Assess effects of CRISPR perturbations alongside single cell gene expression.
Cell Multiplexing
Multiplex up to 12 samples per channel for increased sample throughput.
High Throughput (HT)
Profile 2,000–20,000 cells per channel of the Chromium Next GEM Chip M (2,000– 60,000 cells per channel with CellPlex).
Low Throughput (LT)
Partition 100–1,000 cells per channel efficiently, for up to 8,000 cells per run.
Datasets

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

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Datasets

Videos

Explore how-to videos and training modules.

Chromium Next GEM Single Cell 3' v3.1 - Dual Index video
How-to series
Chromium Next GEM Single Cell 3' v3.1 - Dual Index
Chromium Next GEM Single Cell 3' v3.1 - Single Index video
How-to series
Chromium Next GEM Single Cell 3' v3.1 - Single Index
Chromium Next GEM Single Cell 3' HT v3.1 - Dual Index video
How-to series
Chromium Next GEM Single Cell 3' HT v3.1 - Dual Index
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Q&A

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

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Q&A
Publications

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

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Publications