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 Immune Profiling allows analysis of full-length, paired B-cell or T-cell receptor (BCR/TCR) sequences, surface protein expression, antigen specificity, and 5’ gene expression, all from a single cell. Scale up with a high-throughput solution, or focus on key genes with targeted gene expression panels.

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

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 Immune Profiling

Overview

Documentation

Additional Applications

Datasets

Videos

Publications

<div><Text as={'span'} size={'medium'} weight={'medium'}>{`This assay requires Chromium X/iX instrument Firmware v2.0 or newer. Refer to the `}</Text><Anchor href={'/support/instruments/chromium-x-series/chromium-x-series-firmware-update-procedure'}><Text as={'span'} color={'inherit'} size={'medium'} weight={'medium'}>{'Chromium X Series Firmware Update Procedure'}</Text></Anchor><Text as={'span'} size={'medium'} weight={'medium'}>{' for details'}</Text></div>

Chromium Single Cell Immune Profiling allows analysis of full-length, paired B-cell or T-cell receptor (BCR/TCR) sequences, surface protein expression, and 5’ gene expression, all from a single cell.

What is Single Cell Immune Profiling?

Measure single cell gene expression, cell surface protein expression, and optionally antigen specificity simultaneously.

Cell Surface Protein

Assess the effects of CRISPR perturbations alongside single cell gene expression.

CRISPR Screening

Enables molecular profiling of 2,000–20,000 cells/sample with simultaneous detection of full length, paired immune receptor sequences, gene and protein expression, and antigen specificity.

High Throughput (HT)

Map antigens to discover novel antigen-specific Ig or T-cell receptors.

Barcode Enabled Antigen Mapping (BEAM)

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.

Chromium Next GEM Single Cell 5' v2 Dual Index

Chromium Next GEM Single Cell 5' HT v2 Dual Index

Single Cell 5' v2 Barcode Enabled Antigen Mapping (BEAM)

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

Q&As

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)