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Provides instructions for constructing libraries using the Chromium Next GEM Single Cell 3' Reagent Kit (v3.1).

Chromium Next GEM Automated Single Cell 3ʹ Reagent Kits User Guide (v3.1 Chemistry)

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

Library Construction

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

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

<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 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.

Chromium Next GEM Automated Single Cell 3ʹ Reagent Kits User Guide (v3.1 Chemistry)

User Guide, CG000286

CG000286_ChromiumSingleCell3-_v3.1_Automation_UG_RevF.pdf

User Guide, CG000309

Sample Input File: CG000309_ChromiumConnect_SC3-GEX_InputSampleInfo_Template_RevD.csv

User Guide, CG000435

Input File: CG000435_ChromiumConnect_SC3-GEX_InputFile_RevD.xlsm

User Guide, CG000434

CG000434_ChromiumConnect_qPCR-Setup_InputFile_RevA.xlsm

User Guide, CG000433

CG000433_ChromiumConnect_qPCR-Setup_InputSampleInfo_Template_RevA.csv

User Guide, CG000157

CG000157_ChromiumConnect_LibraryQuantificationWorksheet_RevB.xlsm

User Guide, CG000310

CG000310_ChromiumConnect_Pooling-8Libraries_InputSampleInfo_Template_RevB.csv

User Guide, CG000156

CG000156_ChromiumConnect_PoolingWorksheet_RevC.xlsm

User Guide, CG000435

CG000435_Chromium Connect SC3-GEX Input File_Rev C.xlsm

User Guide, CG000466

CG000466_Chromium Connect 32 Pooling Workbook_Rev A.xlsm

User Guide, CG000485

CG000485_Chromium Connect Library Construction Input File_Rev A.xlsm

User Guide, CG000486

CG000486_Chromium Connect Automation Library Construction LIMS Template_Rev A.csv

User Guide, CG000493

CG000493_Chromium Connect Library Pooling LIMS Template_Rev A.csv