Breaking Barriers to Scaling Single Cell Research with GEM-X Flex v2
By Anna F., Sep
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Single cell sequencing is advancing biomedical research, but scaling studies across large cohorts, longitudinal timepoints or precious clinical samples remains a challenge. From our experience supporting earlier single cell projects, the need to process viable fresh cells promptly often meant bringing our team onsite for cell capture service. Flex changes this. Samples can now be fixed locally and sent to Novogene lab for downstream processing, giving researchers greater flexibility in how and when samples are collected. Building on our experience delivering GEM-X Flex v1, Novogene now offers the next generation Flex v2 service to help researchers overcome the practical barriers to scaling single-cell studies.
Here, we examine four common barriers to scaling single cell research, and how Flex v2 and Novogene’s end-to-end services can help address them.
Challenge 1: Samples are collected at different times and locations
Clinical and longitudinal studies often involve samples collected over several months or across multiple sites. Processing each sample as it arrives can increase run-to-run variation and complicate study coordination.
How Flex v2 helps: Samples can be fixed following collection, stored and processed together later. This enables researchers to consolidate samples into planned batches, helping to reduce processing related technical variation and improve consistency across the cohort.
How Novogene can help: Novogene offers sample fixation services following 10x Genomics protocols. The Flex workflow supports fixed cells and nuclei, FFPE samples, single-cell suspensions, and fresh or frozen tissue, giving researchers greater flexibility in sample collection, storage and submission. This reduces reliance on immediate fresh-sample processing and supports more practical study planning.
Challenge 2: Fresh, viable cells are not always available
Conventional single cell workflows typically require viable fresh cells to be processed promptly. This can be difficult when samples are fragile, collected far from a laboratory or available only as archived tissue.
How Flex v2 helps: Its probe-based workflow supports fixed cells and nuclei as well as FFPE tissue, expanding the range of samples available for single cell analysis. Fresh and frozen material may also be processed using an appropriate fixation or nuclei-isolation workflow. Sample suitability still depends on factors such as tissue type, preservation method and sample quality.
How Novogene can help: Early consultation with our local specialists can help identify the most appropriate single cell service and workflow before valuable samples are collected or submitted.
Challenge 3: Cost can limit cohort size
Budget and workflow constraints often limit the number of samples included in single cell studies. Yet larger cohorts may be needed to capture patient-to-patient variability, compare treatment responses or investigate disease subtypes.
How Flex v2 helps: Each sample is labelled with a unique barcode before pooling, preserving its identity throughout downstream library preparation and sequencing. By enabling multiple samples to be processed together, this multiplexed workflow can streamline sample handling and improve cost efficiency, making larger and potentially more representative cohort studies more accessible.
How Novogene can help: Novogene currently supports up to 23 samples per run within its optimised service workflow for quality assurance. For higher multiplexing request, can followup with team. We have local single cell labs in Singapore, Japan and Hong Kong. Researchers can discuss their study design with our local representatives. Together, we can evaluate sample numbers, sequencing requirements, analysis needs and budget considerations to identify an appropriate workflow for the project.
Challenge 4: More samples create greater analytical complexity
Increasing sample numbers and cellular throughput can generate richer datasets, but it also makes data integration and interpretation more demanding. Reliable comparisons across samples are essential for distinguishing biological differences from technical variation.
How Novogene can help: Novogene provides end-to-end support from cell or nuclei QC and library preparation through to sequencing and bioinformatics analysis. Available analyses include demultiplexing, multi-sample integration, cell-type annotation, differential gene expression, pseudotime analysis, cell–cell communication analysis and more, helping researchers translate complex datasets into meaningful biological findings.
Sample Expertise Across Diverse Tissue Types
As of 2026, Novogene has completed more than 600 Flex single-cell projects involving diverse sample types. These include fixed cells and FFPE samples from heart, lung, bladder, brain tumour, intestinal lymphoma, head and neck squamous cell carcinoma, chordoma and colorectal cancer tissues. Across our broader single cell portfolio, we have experience supporting more than 50 species. Our integrated service covers study design and sample consultation, sample assessment, laboratory processing, sequencing and bioinformatics, supporting researchers from experimental design through to bioinformatics.
Ready to Start Your Single Cell Project?
Explore Novogene’s single cell sequencing services to identify the right workflow for your samples and research objectives. Receive up to 20% off your first Flex V2 project.
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Anna F. is Product Manager for Single-Cell Sequencing and Spatial Transcriptomics at Novogene AMEA, with 9 years of NGS experience gained through technical roles at a Singapore hospital, Illumina and Thermo Fisher Scientific. She draws on this clinical and industry perspective to help researchers navigate complex single-cell and spatial biology projects.