Chromium Single Cell

Flex Gene Expression

GEM-X technology-powered assays with protein coding gene coverage, customizable to fit project needs

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Exceptional performance with challenging samples

Reduced cell input recommendations: 25K

Why choose Flex Gene Expression

Using archival or lower quality samples

Need flexible sample batching

Scale large projects for <1 cent per cell

Assay specifications

Species

Mouse

Human

Other species with custom probes

Compatible samples

Cell suspension

Nuclei suspension

Fresh tissue

Frozen tissue

FFPE tissue

PFA-fixed tissue

Flow-sorted cells

Fixed whole blood

Organoids

Multiomics

Probe-based gene expression

Cell surface protein

Intracellular protein

CRISPR screening

Compatible instruments

Chromium X

Chromium iX

Throughput options

Singleplex

20K cells/sample

160K cells/chip

8 samples/chip

In-line multiplexing

20K cells/sample

2.56M cells/chip

128 samples/chip

Components

Each experiment requires a chip, index kit, and core reagents. If you're unsure what you need, use the experiment builder find the custom list of items required for your experiment.

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Consumables

Choose a version

Nuclei Isolation (optional)

REAGENT

1000494

Chromium Nuclei Isolation with RNase Inhibitor Kit, 16rxns

Sample Prep Kit

REAGENT

1000781

GEM-X Flex Sample Preparation v2 Kit, 48 rxns

Individual Wash Workflow (optional)

REAGENT

1000828

GEM-X Flex Supplemental Wash Kit, 64 rxns

Chip

CHIP

1000791

GEM-X Flex Gene Expression Chip Kit, 4 chips

Index Kit

REAGENT

1000251

Dual Index Kit TS Set A, 96 rxn

REAGENT

1000215

Dual Index Kit TT Set A 96 rxns

Core Reagents

REAGENT

1000792

GEM-X Flex Gene Expression Human, 4 samples

REAGENT

1000793

GEM-X Flex Gene Expression Human 4-plex, 16 samples

REAGENT

1000794

GEM-X Flex Gene Expression Human 16-plex, 64 samples

REAGENT

1000829

GEM-X Flex Gene Expression Human n-plex, 64 samples

REAGENT

1000795

GEM-X Flex Gene Expression Human 16-plex, 256 samples

REAGENT

1000796

GEM-X Flex Gene Expression Mouse, 4 samples

REAGENT

1000797

GEM-X Flex Gene Expression Mouse 4-plex, 16 samples

REAGENT

1000798

GEM-X Flex Gene Expression Mouse 16-plex, 64 samples

REAGENT

1000831

GEM-X Flex Gene Expression Mouse n-plex, 64 samples

REAGENT

1000799

GEM-X Flex Gene Expression Mouse 16-plex, 256 samples

Feature Barcoding Kit (optional)

REAGENT

1000628

Fixed RNA Feature Barcode Multiplexing Kit, 64 rxns

Compatible Instruments

Chromium X Chromium iX

Build your own Flex Gene Expression experiment

Design the experiment that's right for you

Start building

Sequencing requirements

Minimum 10,000 read pairs/cell for gene expression; 5,000 read pairs/cell for protein analysis.

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Analysis guides

Hands-on Tour of the Single Cell Analysis Journey Find software documentation

Grant resources

Create a Letter of Support Grant Application Resources for Chromium GEM-X Single Cell Gene Expression

Demonstrated protocol

Cell Surface & Intracellular Protein Labeling for Chromium Fixed RNA Profiling

Data spotlight

Robust results for scRNA-seq from matched FFPE and freshly fixed samples

Videos

How it works

Change the rules for scRNA-seq: Access more samples, run on your schedule

Single cell analysis of FFPE tissue: Experiences and considerations from a pathologist’s perspective

Direct fixation of whole blood for downstream single cell analysis

High-throughput single cell profiling with streamlined workflows and multiomic readouts at unparalleled scale

Data analysis

Explore analysis software

Cell Ranger

Cell Ranger is a set of free analysis pipelines for processing Chromium Single Cell data

Learn more

Loupe Browser

Loupe Browser is a desktop application for Windows and MacOS that allows you to interactively visualize data

Learn more

Cloud Analysis

Cloud Analysis enables quick and easy access to Cell Ranger pipelines from your web browser

Learn more

Featured publications

View more publications

Single-cell systems pharmacology identifies development-driven drug response and combination therapy in B cell acute lymphoblastic leukemia

Cancer Cell, 2024

Xin Huang, et al.

Read on PubMed

Peroxisome deficiency underlies failures in hepatic immune cell development and antigen presentation in a severe Zellweger disease model

Cell Reports, 2024

Brendon D Parsons, et al.

Read on PubMed

Cortical somatostatin long-range projection neurons and interneurons exhibit divergent developmental trajectories

Neuron, 2023

Josephine Fisher, et al.

Read on PubMed

Featured datasets

View all Flex datasets

10k Mouse Forebrain FFPE Tissue Dissociated using gentleMACS Dissociator, Singleplex Sample

View dataset

Aggregate of ~900k Human Non Small Cell Lung Cancer and Normal Adjacent Cells, Multiplexed Samples, 16 Probe Barcodes

View dataset

128k Human PBMCs Stained with TotalSeq™-C Human Universal Cocktail

View dataset

Human Ovarian Cancer FFPE Single Cell Gene Expression Flex

View dataset

Aggregate of Human PBMC Isolated from Fixed Whole Blood of a Diseased Donor and a Healthy Donor

View dataset

Chromium Single Cell

Flex Gene Expression

Why choose Flex Gene Expression

Assay specifications

Species

Compatible samples

Multiomics

Compatible instruments

Throughput options

Singleplex

In-line multiplexing

Components

Build your own Flex Gene Expression experiment

Documents and resources

Product sheet

Sample prep

User guides

Application notes

Sequencing requirements

Analysis guides

Grant resources

Demonstrated protocol

Data spotlight

Videos

How it works

Change the rules for scRNA-seq: Access more samples, run on your schedule

Single cell analysis of FFPE tissue: Experiences and considerations from a pathologist’s perspective

Direct fixation of whole blood for downstream single cell analysis

High-throughput single cell profiling with streamlined workflows and multiomic readouts at unparalleled scale

Data analysis

Cell Ranger

Loupe Browser

Cloud Analysis

Featured publications

Single-cell systems pharmacology identifies development-driven drug response and combination therapy in B cell acute lymphoblastic leukemia

Peroxisome deficiency underlies failures in hepatic immune cell development and antigen presentation in a severe Zellweger disease model

Cortical somatostatin long-range projection neurons and interneurons exhibit divergent developmental trajectories

Featured datasets

10k Mouse Forebrain FFPE Tissue Dissociated using gentleMACS Dissociator, Singleplex Sample

Aggregate of ~900k Human Non Small Cell Lung Cancer and Normal Adjacent Cells, Multiplexed Samples, 16 Probe Barcodes

128k Human PBMCs Stained with TotalSeq™-C Human Universal Cocktail

Human Ovarian Cancer FFPE Single Cell Gene Expression Flex

Aggregate of Human PBMC Isolated from Fixed Whole Blood of a Diseased Donor and a Healthy Donor

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