Lists compatibility of different species and panel formats with downstream Single Cell Targeted and Spatial Targeted Gene Expression assays.

Targeted Gene Expression Protocol Compatibility Table

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

Targeted

Targeted Gene Expression (Optional)

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

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

Sample Prep

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

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)

Partition 100–1,000 cells per channel efficiently, for up to 8,000 cells per run.

Low Throughput (LT)

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.

Panel type	Panel Vendor & format	Single Cell Gene Expression or Immune Profiling, Human	Single Cell Gene Expression or Immune Profiling, Mouse	Visium Spatial Gene Expression Fresh Frozen, Human	Visium Spatial Gene Expression Fresh Frozen, Mouse
Pre-designed panels	10x Genomics
Add-on panels	IDT xGEN Custom Hyb Panels, IDT NGS Discovery Pools, IDT xGEN Lockdown Probe Pools
Fully custom panels	IDT xGEN Custom Hyb Panels, IDT NGS Discovery Pools, IDT xGEN Lockdown Probe Pools
Fully custom panels	Biotinylated Amplified Twist Oligo Pools (CG000412)