Do more with every sample using 10x Genomics Chromium Flex assays

Great single cell science often starts with a logistics headache. Samples arrive at odd hours, from different sites, in different states. Fresh tissue will not wait, and every extra run adds cost and batch effects.

Chromium Flex from 10x Genomics changes that. Fix your samples when they arrive, process them when it suits you, and pool them into one run for clean, comparable data. Here is how Flex helps you get more from every sample and every grant dollar.

Flex is a probe based, whole transcriptome single cell assay built for fixed samples. Instead of capturing every RNA molecule, Flex uses probe pairs that target more than 18,000 human or mouse genes. Because probes bind short stretches of RNA, Flex delivers sensitive data even when RNA is partially degraded.

A plate-based transformation for high throughput multiplexing

• Sensitive, probe-based whole transcriptome analysis covering more than 18,000 human or mouse genes
• Fix and process samples individually (singleplex workflow) or pooled with up to 384 samples in a single lane of a Chromium chip (plate-based multiplex workflow)
• Multiomic profiling with cell surface protein, intracellular protein, or CRISPR gRNA

That makes Flex a natural fit for samples that are hard to run fresh:

• Fixed cells and nuclei
• Fresh, frozen and fixed tissue
• FFPE tissue blocks
• Whole blood fixed at the point of collection

Fixation also creates a safe stopping point. Collect samples over days or weeks, store them, then process them together in a single batch.

The newest Flex chemistry, Flex Apex, brings a plate based workflow to single cell multiplexing. You can pool up to 384 samples in a single lane of a Chromium chip, so large cohort and screening studies become practical on one instrument.

• Singleplex or multiplex. Fix and process samples individually, or pool them in a plate based workflow.
• Whole transcriptome. Sensitive probe based coverage of more than 18,000 human or mouse genes.
• Multiomic options. Add cell surface protein, intracellular protein or CRISPR gRNA readouts to the same cells.

Pooling more samples per run lowers the cost per sample and reduces batch effects, which strengthens both your data and your next grant application.

• Tracking cancer causing gene fusions. Australian researchers including the Peter MacCallum Cancer Centre have developed Flexify, which designs custom Flex probes for oncogenic gene fusions. In a recent preprint, they used it to find leukaemic cells hiding at minimal residual disease in children with B cell acute lymphoblastic leukaemia. Read the preprint.
• Genome wide CRISPR screens, cell by cell. Researchers at the New York Genome Center developed VIPerturb-seq, which uses Flex probe chemistry to read CRISPR guides in fixed cells. In one screen, they profiled 880,000 cells in a single afternoon. Explore VIPerturb-seq.

Blood is one of the most valuable sample types in clinical research, and one of the hardest to handle. Flex Apex blood protocols stabilise samples at the moment of collection, with no lab access or skilled staff needed on site. Samples can then be processed at a central lab when you are ready.

• Use standard collection tubes. Protocols support PAXgene Blood RNA and Streck Cell Free DNA tubes, which kept stress gene expression markedly lower than EDTA.
• Store and ship with confidence. Depending on the protocol, samples hold at room temperature or 4°C for up to 3 days, or can be frozen long term. PAXgene samples kept their data quality through up to 3 freeze and thaw cycles.
• Unlock archived blood. Run single cell analysis on frozen blood samples from earlier studies.
• Keep the true picture. Immune cell proportions, including granulocytes, stayed comparable across collection methods.
• Batch across sites and time points. Ideal for multi site trials, longitudinal studies and time courses, without adding batch effects.

You can also fix whole blood directly at collection, with only 5 to 15 minutes of hands on time per sample. Read the 10x Genomics blood fixation guide.

Archived FFPE blocks hold decades of research potential. Flex Apex includes a xylene free protocol for deparaffinising and dissociating FFPE scrolls, in tubes or 96 well plates.

• Fast. Process up to 96 samples in under an hour with the plate protocol, or up to 16 samples in individual tubes.
• Consistent. Data quality matched the xylene based workflow across kidney, lung and ovarian tissue, using blocks 1 to 20 years old.
• Proven at scale. 24 distinct FFPE blocks, each run four times in a single 96 plex experiment, gave more than 1 million nuclei with consistent quality.

RNA tells you what a cell could do. Protein tells you what it is doing. The MultiPro® Human Discovery Panel lets you measure both in the same cells, in the same Flex run.

• Broad coverage. 347 DNA barcoded antibodies profile up to 326 human protein targets, plus isotype controls.
• Inside and out. Covers surface and intracellular targets, including cytokines, transcription factors and phosphoproteins.
• Easy to adopt. A pre titrated, lyophilised, single use cocktail that slots into existing GEM‑X Flex workflows.
• Proven on immune samples. Validated on PBMCs, bone marrow mononuclear cells, stimulated immune cells and iPSCs.

Paired with blood fixation, MultiPro gives immunology and translational teams a deep, same cell view of immune state from routine clinical samples.

Ready to try Flex in your lab? For orders placed by 18 December 2026, choose one of these offers with a Flex 16 reaction kit:

• Free MultiPro Human Discovery Panel. Get a free Human Discovery Panel 4 reaction kit with any Human Flex kit, and capture 300+ proteins from the same cells. Limit of one free kit per lab account.
• Free blood tubes and sample prep. Get AUD$1,000 off your Flex order towards blood tubes and Sample Prep v2. Smaller Flex kits get 50% off sample prep.
• Free 10x data analysis course. Claim a free seat, valued at AUD$3,985, in an 8 week online course covering single cell and spatial analysis, with a certificate on completion. Limited to 20 seats across APAC for the next cohort.

One offer per order, and offers cannot be combined.