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Single-cell sequencing

Single-cell sequencing is a collection of advanced biotechnologies that enable the detailed analysis of genomic, transcriptomic, epigenomic, and proteomic profiles from individual cells, uncovering molecular heterogeneity that is obscured in conventional bulk sequencing methods which average data across cell populations.^[1] This approach has revolutionized the understanding of cellular diversity, dynamics, and interactions within tissues and organs, facilitating breakthroughs in precision medicine and biological research.^[1] The origins of single-cell sequencing trace back to early efforts in single-cell transcriptomics, with the first demonstration of whole-transcriptome RNA sequencing (scRNA-seq) achieved by Tang et al. in 2009 using a single mouse blastomere, detecting expression of 5,270 genes—75% more than achieved by contemporary microarray techniques.^[2] Building on this, single-cell whole-genome sequencing emerged in 2011 through Navin et al.'s work, which sequenced DNA from individual nuclei in breast cancer samples to infer tumor evolution and copy number variations.^[3] Subsequent innovations in the 2010s, including Smart-seq2 for improved full-length cDNA amplification and droplet-based systems like Drop-seq (2015), scaled throughput to thousands of cells, while multi-omics methods such as CITE-seq (2017) began integrating RNA and protein data.^[1] Key technologies in single-cell sequencing span several modalities: for genomics, multiple displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC) address whole-genome coverage challenges; transcriptomics relies on scRNA-seq variants like plate-based (e.g., Smart-seq) and high-throughput droplet or microwell methods (e.g., 10x Genomics Chromium); epigenomics includes single-cell bisulfite sequencing (scBS-seq) for DNA methylation and assay for transposase-accessible chromatin (scATAC-seq) for chromatin accessibility.^[1] Unique molecular identifiers (UMIs) and barcoding enhance accuracy by correcting for PCR biases and enabling multiplexing.^[4] Applications of single-cell sequencing are vast and interdisciplinary, including dissecting tumor microenvironments in cancer to identify rare subclones and therapeutic targets, as seen in melanoma and breast cancer studies; mapping immune cell states in infectious diseases like COVID-19; and charting developmental trajectories in embryogenesis and organogenesis.^[1]^[4] Large-scale efforts, such as the Human Cell Atlas initiative launched in 2016, leverage these technologies to catalog all human cell types across tissues, promoting global collaboration in creating reference maps for health and disease.^[5] Despite its advancements, single-cell sequencing faces hurdles like amplification-induced biases, low capture efficiency leading to sparse data, high per-experiment costs, and computational demands for integrating multi-omics datasets and inferring cell trajectories.^[1] Ongoing developments in spatial transcriptomics and long-read sequencing promise to address these limitations, further expanding the field's impact.^[4]

Introduction

Definition and principles

Single-cell sequencing encompasses a suite of high-throughput next-generation sequencing (NGS) techniques applied to individual cells to profile their genomic, transcriptomic, epigenomic, or multi-omic features, thereby unveiling cellular heterogeneity within complex populations that bulk methods cannot resolve.^[1] This approach enables the detection of molecular variations at the single-cell level, such as differences in DNA copy number, RNA expression, or chromatin accessibility, which are critical for understanding tissue diversity, developmental processes, and disease states.^[6] At its core, single-cell sequencing operates on principles of isolating individual cells from a sample, lysing them to access nucleic acids, amplifying the target molecules while minimizing bias, and incorporating barcodes or unique molecular identifiers (UMIs) to enable multiplexing and traceability during NGS.^[4] These steps allow for the precise quantification of molecular content per cell, highlighting advantages like the identification of rare subpopulations, transient cellular states, and stochastic gene expression fluctuations that are obscured in population-level averages. For instance, the inaugural single-cell RNA sequencing experiment demonstrated the ability to detect the expression of over 5,000 genes from individual mouse oocytes and blastomeres, exposing expression heterogeneity not detectable in bulk analyses.^[7] In contrast to bulk sequencing, which pools nucleic acids from thousands to millions of cells and yields an averaged signal masking intra-population diversity, single-cell sequencing captures cell-to-cell variability, including transcriptional noise and subclonal mutations.^[1] This distinction is exemplified in early single-cell DNA sequencing applications, where analysis of individual tumor cell nuclei revealed punctuated clonal expansions and genetic substructures in breast cancers, providing insights into tumor evolution unattainable through bulk tumor profiling.^[3] The basic workflow of single-cell sequencing generally proceeds from cell isolation—using techniques such as fluorescence-activated cell sorting or microfluidic encapsulation—to lysis and nucleic acid capture, followed by reverse transcription or amplification, barcoded library preparation, and deep NGS to generate per-cell molecular profiles.^[6]

Historical development

The roots of single-cell sequencing lie in early methods for probing gene expression at the individual cell level. In the 1990s, single-cell quantitative PCR (qPCR) techniques were developed to quantify the expression of a small number of genes, offering the first glimpses into cellular heterogeneity without the averaging effects of bulk analyses.^[8] The introduction of next-generation sequencing (NGS) platforms around 2005, including the 454 sequencer and Illumina's Genome Analyzer, marked a critical enabling step by providing scalable, high-throughput DNA sequencing capabilities that would later support single-cell applications.^[9] A landmark achievement came in 2009 with the first demonstration of single-cell RNA sequencing (scRNA-seq) by Tang et al., who sequenced the transcriptome of individual mouse blastomeres using a method involving mRNA capture via oligo(dT) priming and in vitro transcription for linear amplification, followed by NGS.^[7] This proof-of-concept overcame key technical hurdles in amplifying and sequencing minute amounts of cellular RNA, setting the stage for broader adoption. The 2010s saw rapid innovations in throughput and automation. In 2012, Fluidigm launched the C1 Integrated Fluidic Circuit system, which automated single-cell capture, lysis, and cDNA synthesis in microfluidic chips, enabling consistent processing of dozens to hundreds of cells. Droplet-based methods further scaled the technology: in 2015, Macosko et al. introduced Drop-seq, a scalable approach encapsulating cells and barcoded beads in oil droplets for massively parallel scRNA-seq of thousands of cells.^[10] That same year, Klein et al. developed inDrop, an improvement using hydrogel beads for more efficient barcoding and encapsulation, achieving similar high-throughput profiling.^[11] In 2016, 10x Genomics commercialized the Chromium platform, building on these principles to deliver commercial-grade, droplet-based single-cell analysis kits. Single-cell DNA sequencing (scDNA-seq) emerged in the early 2010s, primarily through whole-genome amplification techniques like multiple displacement amplification to detect copy number variations (CNVs) in cancer cells, as exemplified by Navin et al.'s 2011 study mapping genomic heterogeneity in breast tumors. In epigenomics, the 2013 development of single-cell bisulfite sequencing (scBS-seq) by Guo et al. allowed genome-wide DNA methylation profiling from individual cells, revealing epigenetic diversity in early embryos. This was followed in 2015 by Buenrostro et al.'s single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq), which mapped open chromatin regions to infer regulatory states at single-cell resolution.^[12] Multi-omics integration advanced in the late 2010s, with CITE-seq introduced in 2017 by Stoeckius et al. to simultaneously measure RNA transcripts and surface proteins via oligonucleotide-tagged antibodies, enhancing phenotypic resolution. The 2020s brought spatial and multi-modal extensions, combining single-cell sequencing with in situ technologies to preserve tissue context. By 2025, state-of-the-art systems routinely profile over 1 million cells per run, with increasing integration of artificial intelligence for enhanced data interpretation and noise reduction.

Core Technologies

Cell isolation techniques

Cell isolation is a critical initial step in single-cell sequencing, enabling the physical separation of individual cells from heterogeneous samples such as tissues or cultures to facilitate downstream molecular analysis. Various techniques achieve this isolation by leveraging physical, optical, or biochemical properties, each balancing factors like throughput, cell viability, purity, and preservation of native states. These methods are essential for minimizing contamination from neighboring cells and ensuring high-quality single-cell profiles, particularly in applications like transcriptomics and genomics.^[13] Fluorescence-activated cell sorting (FACS) employs fluorescently labeled antibodies to target specific cell surface markers, using laser excitation and light scatter detection to sort viable cells into collection tubes or plates based on size, granularity, and fluorescence intensity. This technique achieves high purity exceeding 95% and throughput rates up to 10,000 cells per second, making it suitable for large-scale isolation from dissociated samples, though it can induce stress due to high-pressure ejection and requires cell labeling that may alter viability. FACS has been widely adopted for single-cell sequencing since its adaptation for multi-parametric sorting in the 1990s, as demonstrated in early applications for hematopoietic stem cell enrichment.^[14]^[15] Magnetic-activated cell sorting (MACS) utilizes superparamagnetic beads coated with antibodies that bind to cell surface antigens, allowing separation via a magnetic field that retains labeled cells on a column while unlabeled cells pass through. It offers gentle handling with cell viabilities often above 90%, scalability for 10^6 to 10^8 cells per run, and lower cost compared to FACS, though it provides binary (positive/negative) selection with less resolution for multiple markers and potential non-specific binding. MACS is particularly useful for enriching rare cell populations prior to single-cell sequencing, as shown in protocols for isolating tumor-infiltrating lymphocytes.^[16]^[17] Microfluidic approaches, including droplet encapsulation, integrate cell partitioning within microchannels or oil-in-water emulsions to isolate thousands to millions of cells in parallel. In droplet-based systems like those used in 10x Genomics platforms, cells are co-encapsulated with barcoded beads in nanoliter-scale droplets, enabling automated, high-throughput isolation (up to 10,000 cells per sample) with minimal manual handling and reduced cross-contamination. These methods excel in scalability and integration with lysis and amplification but require uniform cell suspensions and can suffer from droplet instability or doublets. Seminal droplet technologies, such as Drop-seq and inDrop, revolutionized single-cell transcriptomics by achieving encapsulation efficiencies of 5-10% for input cells.^[10]^[18]^[19] Laser capture microdissection (LCM) involves mounting tissue sections on a thermoplastic film and using an infrared or UV laser to selectively cut and catapult specific cells or regions into a collection cap, preserving spatial context from fixed or frozen samples. It provides precise isolation of hundreds of cells per session with minimal dissociation artifacts but is low-throughput and labor-intensive, with risks of RNA degradation in archival tissues. LCM is ideal for heterogeneous tissues like tumors, where it has enabled single-cell genomic profiling since its development in the late 1990s.^[20]^[21] Manual picking employs micromanipulators or micropipettes under an inverted microscope to aspirate individual cells from a monolayer or suspension, offering high precision for rare or morphologically distinct cells without labels. This method yields near-100% purity but is extremely low-throughput (tens of cells per hour) and operator-dependent, limiting its use to small-scale experiments like validating sequencing results. It remains a gold standard for isolating viable primary cells, as in protocols for neuronal subtypes.^[22] Emerging label-free techniques, such as dielectrophoresis (DEP) and acoustic sorting, exploit intrinsic cell properties to avoid antibody-based labeling. DEP uses non-uniform electric fields to manipulate cells based on their dielectric properties, enabling on-chip isolation of single cells with throughputs of hundreds per minute and viabilities over 90%, suitable for sensitive applications like stem cell sorting. Acoustic methods apply standing surface acoustic waves to separate cells by size or compressibility in microfluidic channels, achieving high purity (up to 99%) and gentle handling at rates of 100-1,000 cells per second without physical contact. These approaches are gaining traction for scalable, non-invasive isolation in single-cell sequencing workflows.^[23]

Library preparation and sequencing platforms

Library preparation for single-cell sequencing begins with the lysis of isolated cells to release nucleic acids, followed by capture of target molecules such as mRNA via poly-A tail selection for transcriptomic analysis.^[24] Reverse transcription then converts RNA to cDNA, often incorporating unique molecular identifiers (UMIs) to tag individual transcripts and mitigate amplification biases during subsequent PCR steps.^[25] Barcoding is applied at the cellular level using combinatorial indices, enabling multiplexing of thousands of cells in a single sequencing run, while targeted amplification enriches libraries for high-throughput next-generation sequencing (NGS).^[6] For single-cell genomic sequencing, whole-genome amplification (WGA) is essential to generate sufficient DNA from limited input, with methods like multiple displacement amplification (MDA) providing uniform coverage through isothermal strand-displacement synthesis, though it can introduce chimeric artifacts, or degenerate oligonucleotide-primed PCR (DOP-PCR) for higher-resolution copy number variant detection via PCR-based enrichment of genome regions.^[26] In transcriptomic workflows, cDNA synthesis techniques vary by coverage needs: Smart-seq2 enables full-length transcript capture using template-switching oligo during reverse transcription, ideal for isoform analysis, while CEL-seq focuses on 3'-end tagging for cost-effective gene counting with linear amplification via in vitro transcription to reduce bias.^[27]^[28] Key platforms for library preparation integrate these steps with automation for scalability. The 10x Genomics Chromium system employs droplet-based microfluidics with Gel Bead-in-Emulsion (GEM) technology, encapsulating up to 100 million cells weekly alongside barcoded beads for UMI and cell indexing with the Chromium Flex as of 2025, a leading provider with major players collectively holding 70-75% market share.^[29]^[30]^[31] Plate-based approaches like the Fluidigm C1 system process 96 to 800 cells in integrated fluidic circuits with optional imaging for viability confirmation, suitable for lower-throughput experiments.^[32] Open-source droplet methods, such as Drop-seq, use simple microfluidic devices to barcode thousands of cells cost-effectively via aqueous nanoliter droplets, while inDrop employs hydrogel-encapsulated primers for similar high-throughput barcoding.^[33]^[34] Kit-based solutions like Parse Biosciences' Evercode platform enable scalable preparation up to 5 million cells per run without specialized instruments, leveraging combinatorial split-pool barcoding for accessibility in academic settings.^[35]^[36] Sequencing of these barcoded libraries typically relies on short-read platforms like the Illumina NovaSeq, which delivers high-throughput output (up to 6 Tb per run) for demultiplexing and read alignment in single-cell applications.^[37] Emerging long-read technologies, including PacBio's high-fidelity circular consensus sequencing and Oxford Nanopore's direct nanopore readout, are increasingly adapted for single-cell use to resolve full-length transcripts and isoforms, though they currently offer lower throughput compared to short-read systems.^[38]

Single-cell genomic sequencing

Methods

Single-cell genomic sequencing focuses on analyzing the DNA sequence, structure, and variations within individual cells to uncover genetic heterogeneity masked in bulk samples. Key methods rely on whole-genome amplification (WGA) to generate sufficient DNA from the limited input (typically 1-10 pg per cell) for high-throughput sequencing. Early techniques include degenerate oligonucleotide-primed PCR (DOP-PCR), which uses semi-random primers for initial amplification but suffers from uneven coverage. Multiple displacement amplification (MDA) employs phi29 DNA polymerase for isothermal amplification, achieving higher fidelity and ~50% genome coverage at 20× depth, as demonstrated in studies of B lymphocyte mutations.^[1] Improved methods like multiple annealing and looping-based amplification cycles (MALBAC) reduce bias by forming DNA loops to prevent over-amplification of early products, enabling better uniformity for copy number variation (CNV) detection. The first single-cell whole-genome sequencing was reported by Navin et al. in 2011, sequencing DNA from breast cancer cell nuclei to infer tumor evolution and subclonal CNVs using MDA.^[3] Subsequent platforms, such as Fluidigm's C1 system (introduced 2013), automate cell isolation and WGA for scalable processing.^[1] High-throughput approaches incorporate barcoding for multiplexing, including the 10x Genomics Chromium for CNV profiling and Mission Bio's Tapestri for targeted sequencing of mutations in hematologic cancers. Recent advances as of 2025 emphasize long-read technologies to resolve structural variants (SVs) and haplotypes. For instance, single-cell multiple displacement amplification with direct long-read sequencing (dMDA) generates reads up to 10 kb, achieving ~40% coverage with 15.7 Gb of data, while SMOOTH-seq enables de novo genome assembly from ~30 cells with contig N50 lengths of ~1.35 Mb. These methods, using PacBio or Oxford Nanopore platforms, detect 16-fold more SVs than short-read approaches and support phasing with fewer than 100 cells.^[39] Single-nucleus isolation is often preferred for solid tissues to avoid DNA damage during dissociation.^[1]

Limitations

Single-cell genomic sequencing is challenged by technical biases and inefficiencies inherent to WGA from minute DNA quantities. Amplification bias leads to uneven coverage, with MDA and DOP-PCR showing chimeric artifacts and allelic dropout rates up to 30-50%, where one allele fails to amplify, complicating variant calling and heterozygosity detection. MALBAC mitigates this but still achieves only ~70-90% uniformity compared to bulk sequencing.^[1] Coverage sparsity is prevalent, often limited to 10-50% of the genome per cell at practical depths (e.g., 0.1-1× average), requiring deep sequencing (15-30 Gb per cell) for reliable CNV or mutation detection, which escalates costs to $1-5 per cell for short-read methods and higher for long-read. Long-read approaches as of 2025 improve resolution for repeats and SVs but face low throughput (<100 cells per run) and error rates (1-5% for early Oxford Nanopore), though recent iterations reach >99% accuracy. Computational demands for assembling fragmented, biased data and correcting errors remain high, with haplotype phasing feasible only in low-heterozygosity samples. These issues limit applications to targeted panels over full genomes in routine use.^[39]^[40]

Applications

Single-cell genomic sequencing reveals intratumor genetic diversity and evolutionary dynamics, aiding precision oncology. In breast cancer, it has mapped CNVs and subclones to trace tumor progression and metastasis, identifying therapy-resistant variants. Similarly, in acute myeloid leukemia (AML), targeted sequencing tracks clonal evolution under FLT3 inhibitor treatment, informing relapse mechanisms.^[1] Beyond cancer, it detects somatic mosaicism in neurodevelopment, sequencing hundreds of neurons to uncover low-frequency mutations linked to epilepsy and autism. In infectious diseases, it profiles pathogen integration in host genomes, such as HIV proviral loads in immune cells. Large consortia like the Human Cell Atlas incorporate scWGS for baseline genetic maps across tissues. As of 2025, long-read methods enable whole-chromosome phasing in embryos, advancing reproductive genetics and de novo mutation studies in rare diseases. These applications highlight its role in dissecting genetic heterogeneity at cellular resolution.^[39]^[5]

Single-cell transcriptomic sequencing

Methods

Single-cell transcriptomic sequencing, primarily through single-cell RNA sequencing (scRNA-seq), captures the transcriptome of individual cells to reveal gene expression heterogeneity. Key methods include plate-based approaches, such as Smart-seq2, which amplify full-length cDNA from polyadenylated mRNA using template-switching oligo technology, enabling detailed isoform and allele-specific expression analysis but limited to lower throughput (hundreds of cells).^[41] Droplet-based methods, like Drop-seq and the 10x Genomics Chromium platform, encapsulate single cells with barcoded beads in oil droplets for high-throughput profiling of thousands to millions of cells, typically capturing 3'-end transcripts with unique molecular identifiers (UMIs) to mitigate amplification biases.^[42] Microwell-based systems, such as Microwell-seq, offer cost-effective alternatives by loading cells and barcoded primers into arrays of sub-nanoliter wells, supporting scalable 3'-end sequencing with reduced reagent use.^[43] Combinatorial indexing techniques, including SPLiT-seq, further enhance throughput by applying multiple rounds of barcoding without physical cell partitioning, enabling profiling of up to 100,000 cells per experiment as of 2023 advancements.^[44] Cell isolation precedes library preparation, often via fluorescence-activated cell sorting (FACS) or microfluidics, followed by reverse transcription, amplification, and sequencing on platforms like Illumina NovaSeq. Recent 2025 developments, such as optimized Smart-seq3 variants, improve capture efficiency for low-input samples, achieving near-full-length coverage in diverse tissues.^[45]

Limitations

Single-cell transcriptomic sequencing faces challenges related to technical variability and data sparsity. Capture efficiency is typically low, around 10-20% of the transcriptome per cell, leading to dropout events where low-expressed genes appear undetected, complicating differential expression analysis.^[42] Amplification biases from methods like multiple displacement amplification introduce noise, particularly in full-length protocols, while droplet-based approaches suffer from doublets (two cells in one droplet) at rates of 1-5%, requiring computational filtering.^[46] The dissociation of tissues for single-cell suspension can alter transcriptomic states, introducing stress responses or losing fragile cell types, and the method inherently discards spatial information, necessitating integration with spatial transcriptomics for context.^[47] High costs, estimated at $0.50-2 per cell for large-scale runs as of 2025, and computational demands for processing sparse matrices (often 80-90% zeros) limit accessibility, though open-source tools like Seurat mitigate analysis barriers.^[48]

Applications

Single-cell transcriptomic sequencing has transformed biological research by enabling high-resolution mapping of cell types and states. In cancer, scRNA-seq dissects tumor heterogeneity, identifying rare subclones and therapy-resistant populations, as in breast cancer studies revealing evolutionary trajectories.^[49] In immunology, it profiles immune responses, such as T-cell exhaustion in COVID-19, uncovering dynamic shifts in cytokine expression across infection stages.^[50] Developmental biology benefits from trajectory inference, tracing lineage decisions in embryogenesis, exemplified by atlases of human gastrulation highlighting regulatory networks.^[51] Neurological applications include charting brain cell diversity, linking transcriptomic signatures to disorders like Alzheimer's via integration with genetic data. As of 2025, large consortia like the Human Cell Atlas incorporate scRNA-seq for comprehensive tissue maps, advancing precision medicine through biomarker discovery.^[5]

Single-cell epigenomic sequencing

Methods

Single-cell epigenomic sequencing methods primarily target DNA methylation and chromatin accessibility to reveal epigenetic heterogeneity across individual cells. For DNA methylation profiling, single-cell bisulfite sequencing (scBS-seq) involves cell lysis followed by bisulfite conversion to deaminate unmethylated cytosines, enabling differentiation from methylated ones during subsequent whole-genome amplification and sequencing. This approach, often using post-bisulfite genome tagging (PGT) for library preparation, typically covers only 1-10% of CpG sites per cell due to inefficiencies in amplification and conversion, limiting genome-wide resolution but allowing detection of methylation patterns in rare cell types. Early implementations demonstrated accurate measurement at up to 48.4% of CpGs in optimized cases, highlighting its utility for assessing epigenetic variability in development and disease.^[52] Chromatin accessibility is commonly assayed using single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq), which employs the Tn5 transposase to insert sequencing adapters into open chromatin regions via tagmentation, typically performed on isolated nuclei to preserve structure. Following tagmentation, Nextera-based library preparation incorporates cellular barcodes—often integrated via combinatorial indexing strategies—to enable multiplexing and demultiplexing of thousands of cells. This method generates 1,000 to 50,000 unique reads per cell, sufficient to identify accessible regulatory elements like promoters and enhancers, though coverage sparsity necessitates computational imputation for deeper insights. scATAC-seq has been pivotal in mapping regulatory landscapes in diverse tissues, revealing cell-type-specific transcription factor motifs.^[53] Variants of these core methods expand profiling capabilities while addressing scalability. For instance, single-cell nucleosome, methylation, and transcription sequencing (scNMT-seq) combines nucleosome positioning via GpC methyltransferase labeling of accessible regions with bisulfite conversion for methylation and poly-A capture for transcripts, providing integrated epigenomic views from the same cell, though focused here on its epigenetic components. Similarly, single-cell combinatorial indexing ATAC-seq (sci-ATAC-seq) enhances throughput by using split-pool barcoding to profile chromatin accessibility in up to tens of thousands of cells per run, reducing costs and enabling population-scale epigenomic atlases without sacrificing single-cell resolution.^[54] These indexed approaches build on nuclei isolation techniques to minimize dissociation artifacts and integrate barcoding during library preparation for efficient sequencing.^[54] Single-nucleus protocols are essential for epigenomic sequencing of solid tissues like brain, where whole-cell dissociation can introduce biases from incomplete lysis or cytoplasmic contamination, altering perceived accessibility or methylation signals.^[55] By isolating intact nuclei, these methods preserve epigenetic marks in post-mortem or frozen samples, facilitating unbiased profiling of neuronal diversity and disease-associated changes.^[55] Recent advancements, such as sciMETv3 introduced in 2024, enable atlas-scale single-cell DNA methylation profiling through combinatorial indexing, supporting applications in fixed or archived samples to broaden accessibility for longitudinal studies.^[56] This method achieves high-throughput coverage of millions of CpGs across tens of thousands of cells, improving efficiency over earlier bisulfite-based techniques while maintaining compatibility with diverse sample types.^[56]

Limitations

Single-cell epigenomic sequencing encounters challenges related to low input material, amplification biases, and data sparsity. For scBS-seq, bisulfite conversion efficiency is typically 90-95%, but whole-genome amplification introduces allele dropout and biases toward high-CG regions, resulting in uneven coverage and detection of only 1-20% of CpGs on average, with many cells showing zero methylation calls at low-input sites.^[57] These issues limit resolution for global methylation landscapes, particularly in non-CpG contexts, and require deep sequencing (often >100 million reads per cell) to mitigate noise, increasing costs to $10-50 per cell. scATAC-seq suffers from high sparsity, capturing only 1-10% of open chromatin regions per cell due to low fragment recovery (often <5% relative to bulk), leading to 80-90% zero counts in feature matrices and challenges in distinguishing true accessibility from technical noise.^[58] Nuclei isolation helps reduce biases in solid tissues but can miss cytoplasmic factors influencing chromatin, while multiplexing introduces barcode collisions (up to 10-20% in high-throughput runs). Computational demands for peak calling and imputation are high, as sparse data hampers motif discovery and trajectory inference without advanced denoising.^[59] Overall, these methods yield lower throughput than transcriptomics (typically 1,000-10,000 cells per run versus 10,000+), with per-cell costs 2-5 times higher due to specialized reagents. Integration with other modalities remains limited by technical variability, though ongoing improvements in long-read sequencing aim to enhance coverage as of 2025.^[39]

Applications

Single-cell epigenomic sequencing uncovers epigenetic diversity driving cellular identity and disease, enabling mapping of methylation patterns and accessible regulatory elements at individual-cell resolution. In cancer, scBS-seq and scATAC-seq dissect tumor heterogeneity by identifying methylation signatures in rare subclones and chromatin remodeling in therapy-resistant cells; for example, in glioblastoma, scATAC-seq revealed enhancer rewiring in glioma stem cells linked to invasion.^[60] These insights guide precision oncology by pinpointing epigenetic vulnerabilities for demethylating agents like decitabine. In developmental biology, methods like scNMT-seq and snATAC-seq chart epigenetic trajectories during embryogenesis, such as nucleosome positioning and DNA methylation waves in mouse neural progenitors, illuminating how chromatin states dictate lineage commitment.^[61] Applied to human fetal brain tissues, these approaches have cataloged cell-type-specific enhancers associated with neurodevelopmental disorders like autism, linking variants to regulatory disruptions.^[55] In immune responses, single-cell epigenomics profiles dynamic chromatin accessibility in T cell activation, revealing locus-specific opening during differentiation in COVID-19 patients. Large initiatives like the Human Cell Atlas incorporate epigenomic data to create reference maps of tissue-specific methylation, aiding biomarker discovery for autoimmune diseases as of 2025.^[62] Recent advances, including sciMETv3, have extended applications to archived biobanks, enabling retrospective studies of epigenetic drift in aging and environmental exposures.^[56]

Single-cell multi-omics sequencing

Methods and approaches

Single-cell multi-omics methods enable the simultaneous profiling of multiple molecular layers, such as transcripts, proteins, chromatin states, and genetic perturbations, from individual cells to uncover regulatory mechanisms and cellular heterogeneity. These integrated protocols typically leverage shared barcoding strategies or compartmentalization to link modalities without sacrificing throughput, distinguishing them from unimodal assays by providing direct correlations within the same cell. Paired assays combine transcriptomics with proteomics or epigenomics using antibody-based capture. CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by Sequencing) pairs poly-A mRNA capture with oligo-tagged antibodies for surface proteins, allowing quantitative measurement of both transcriptomes and up to hundreds of epitopes in thousands of cells via droplet-based sequencing. Developed by Stoeckius et al. in 2017, this approach has become a standard for dissecting immune cell states by correlating surface markers with gene expression. Similarly, REAP-seq (RNA Expression and Protein Sequencing) extends this paradigm to include intracellular or epigenetic targets, using barcoded antibodies alongside RNA barcoding to profile proteins and transcripts in parallel, as demonstrated by Peterson et al. in 2017 for analyzing T-cell responses. Split-nucleus approaches physically separate nuclear and cytoplasmic components to access distinct layers while preserving single-cell resolution. scNMT-seq (single-cell Nucleosome, Methylation, and Transcription sequencing), introduced by Clark et al. in 2018, isolates intact nuclei for parallel assay of nucleosome positioning via MNase digestion, DNA methylation by bisulfite conversion, and nuclear transcripts, yielding multi-modal profiles from ~1,000 cells to link epigenetic modifications to transcriptional activity in embryonic stem cells.^[63] Building on this, SHARE-seq (Simultaneous High-throughput ATAC and RNA Expression with sequencing), developed by Ma et al. in 2020, employs split-pool combinatorial indexing on permeabilized nuclei to jointly capture open chromatin via Tn5 tagmentation and poly-A RNA, enabling scalable profiling of regulatory elements and expression in >10,000 cells per run and revealing chromatin "potential" in lineage priming.^[64] Perturb-seq integrates functional genomics by coupling CRISPR perturbations with multi-omics readout. This method captures synthetic guide RNA barcodes alongside single-cell RNA profiles in pooled screens, allowing perturbation effects to be deconvolved at transcriptome resolution. Pioneered by Dixit et al. in 2016, Perturb-seq screened ~2,000 guide RNAs in immune cells to map transcriptional responses and regulatory circuits, scaling to genome-wide assessments in subsequent iterations.^[65] Spatial multi-omics methods embed multi-modal capture in tissue context to map molecular interactions across microenvironments. The Visium HD platform from 10x Genomics, launched in 2024 and enhanced in 2025, uses high-density barcoded slides (2 μm resolution) for whole-transcriptome RNA profiling combined with oligo-tagged antibodies for protein detection, supporting unbiased spatial analysis of frozen or FFPE tissues at near-single-cell scale.^[66] For epigenomic integration, adaptations of Slide-seq enable spatial co-profiling of chromatin accessibility and transcripts; Bao et al.'s 2023 method transfers tissue sections for joint ATAC-seq and RNA-seq, achieving ~100 μm resolution to visualize epigenetic landscapes in mouse brain and tumors.^[67] High-throughput platforms streamline multi-omics via commercial droplet systems for massive parallelization. The 10x Genomics Chromium Multiome ATAC + Gene Expression assay, introduced in 2020, partitions nuclei into droplets for simultaneous GEX library preparation and ATAC tagmentation, capturing linked RNA and chromatin accessibility from up to 10,000 nuclei per sample to infer enhancer-gene connections in diverse tissues.^[68] Extensions incorporate reporters like GFP for protein tracking.

Limitations

Single-cell multi-omics sequencing faces significant challenges in correlating multiple data types due to inherent technical discrepancies between modalities. A primary issue is modality mismatch, stemming from varying capture efficiencies; for instance, single-cell RNA sequencing (scRNA-seq) typically captures about 10% of transcripts per cell, while single-cell ATAC sequencing (scATAC-seq) achieves substantially lower efficiency, often recovering less than 5% of accessible chromatin fragments relative to bulk methods.^[42]^[69] This disparity results in 20-50% of cells exhibiting discordant profiles across modalities during integration, as RNA and chromatin signals fail to align reliably, particularly in paired datasets where nuclear isolation for ATAC-seq may alter transcriptomic states.^[70] Noise levels are elevated in multi-omics approaches, exacerbating correlation difficulties. In CITE-seq, which combines transcriptomics with surface proteomics, antibody cross-reactivity introduces false associations, with nonspecific binding leading to spurious protein-RNA correlations and elevated false discovery rates in up to 10-20% of features.^[71] Split-pool methods, used to assay multiple layers sequentially, further compound noise by decoupling measurements from the same cell, losing precise spatiotemporal co-localization and amplifying batch effects between modalities.^[40] Throughput reductions are common, as integrating multiple assays demands more complex library preparation and sequencing depth allocation. For example, commercial kits like 10x Genomics Multiome process up to 10,000 cells per run for combined scRNA-seq and scATAC-seq, compared to higher capacities in single-modality scRNA-seq with newer platforms. This limitation drives up costs, with multi-omics workflows estimated at ~$0.05-0.25 per cell as of 2025, versus ~$0.01-0.10 for optimized single-omics, due to specialized reagents and extended sequencing needs.^[72]^[73] Data sparsity is amplified in combined multi-omics profiles, where individual modalities already exhibit high zero counts—often 80-90% in scRNA-seq alone—resulting in over 70% zeros across integrated datasets, hindering downstream correlation and imputation.^[74] Incorporating spatial multi-omics exacerbates this by introducing resolution loss; many platforms operate at sub-cellular or 50-100 μm pixel scales, averaging signals from multiple cells and diluting modality-specific details.^[75] As of 2025, long-read multi-omics can profile thousands of cells per experiment, as aligning and assembling long reads (e.g., 6-10 kb) across transcriptomic, epigenomic, and genomic layers generates terabytes of data requiring intensive processing resources.^[76]

Applications

Single-cell multi-omics sequencing enables a comprehensive dissection of cellular heterogeneity by integrating transcriptomic, epigenomic, and other molecular layers, offering insights into regulatory mechanisms and functional states within complex biological systems that single-modality approaches cannot achieve. This holistic perspective is particularly valuable for elucidating dynamic interactions in heterogeneous environments, such as those involving cell-cell communication, developmental trajectories, and responses to perturbations or environmental stresses.^[77] In the tumor microenvironment, single-cell multi-omics technologies like CITE-seq have revealed intricate immune-tumor interactions, including the role of PD-L1+ M2-like macrophages in promoting immune exclusion and tumor progression. For instance, CITE-seq profiling identified a spatial niche where these macrophages colocalize with stem-like tumor cells, correlating with CD8 T cell exclusion and adverse clinical outcomes in various cancers. This integration of surface protein and transcriptome data highlights immunosuppressive networks that drive therapy resistance, informing targeted interventions to disrupt these interactions.^[77] During neurodevelopment, scNMT (single-cell nucleosome, methylation, and transcription) sequencing has mapped gene-regulatory links across cortical layers, providing a multi-layered view of how epigenetic modifications orchestrate cell-type diversification. Applied to human cortical nuclei, scNMT datasets from over 63 cell types uncovered regulatory genome diversity, linking distal enhancers and promoters to disease-associated variants in excitatory neurons and interneurons. These findings illuminate the epigenetic-transcriptional dynamics underlying laminar organization and vulnerability to neurodevelopmental disorders.^[78] In assessing immunotherapy responses, Perturb-seq and its multi-omics extensions, such as Multiome Perturb-seq, evaluate the effects of genetic editing in CAR-T cells by simultaneously capturing perturbation-induced changes in gene expression and chromatin accessibility. Genome-wide CRISPR screens using these methods in CAR-T platforms like CELLFIE have identified enhancers of T cell persistence and antitumor efficacy, revealing regulatory circuits that mitigate exhaustion and improve outcomes in hematologic malignancies. This approach deciphers how edits modulate multifunctional states, guiding optimization of next-generation CAR-T therapies.^[79]^[80] For organoids, the 10x Genomics Multiome assay validates tissue mimicry by jointly profiling RNA expression and chromatin accessibility, enabling comparison of in vitro structures to native tissues. In colorectal tumor organoids, Multiome analysis of matched patient-derived samples distinguished cancer-specific cell states and trajectories absent in healthy organoids, confirming their fidelity in recapitulating tumor heterogeneity and stromal interactions. Such applications underscore organoids' utility as models for testing therapeutic responses while quantifying deviations from in vivo architecture.^[81] Recent advances in 2025 have applied single-cell transcriptomics to coral regeneration under climate stress, using scRNA-seq to uncover molecular mechanisms in reef ecosystems. In stony corals like Acropora muricata, these methods revealed cellular dynamics enhancing thermotolerance and regeneration post-bleaching.^[82]^[83]

Data Analysis

Preprocessing and quality control

Preprocessing and quality control in single-cell sequencing involve initial steps to process raw sequencing reads, assess data quality, filter artifacts, and normalize counts to ensure downstream analyses reflect true biological variation rather than technical noise.^[84] These steps are crucial for handling the high-dimensional, sparse nature of single-cell data, where technical factors like sequencing depth and contamination can dominate signals.^[85] Read processing begins with demultiplexing FASTQ files using cell barcodes and unique molecular identifiers (UMIs) to assign reads to individual cells, followed by error correction to mitigate sequencing inaccuracies.^[86] For RNA sequencing, reads are typically aligned to a reference genome using spliced aligners like STAR, which accommodates introns and improves mapping accuracy in transcriptomic data.^[87] In DNA sequencing contexts, such as single-cell ATAC-seq, unspliced aligners like BWA are employed for precise genomic alignment.^[88] Quality control metrics guide cell identification and filtering. Cell calling in droplet-based methods often uses knee plots to distinguish true cells from empty droplets by plotting barcode rank against UMI counts, typically retaining barcodes above an inflection point.^[89] Low-quality cells are filtered based on metrics such as detecting fewer than 200-500 genes per cell, indicating poor capture efficiency, or exceeding 20% mitochondrial gene content, which suggests cellular stress or apoptosis.^[84]^[85] Doublets, arising from multiple cells being encapsulated together, are detected and removed using tools like Scrublet, which simulates doublets and scores them above 0.5 for exclusion.^[90] Additional filtering targets ambient RNA contamination, where free-floating transcripts from lysed cells inflate counts; methods like SoupX estimate and subtract this background by modeling non-cell-associated RNA profiles.^[91] Cells with fewer than 1,000 reads are commonly removed to eliminate those with insufficient coverage.^[89] Normalization adjusts for variations in sequencing depth and library size. For scRNA-seq, log-normalization scales counts by total reads per cell, while SCTransform employs a regularized negative binomial model to stabilize variance and account for technical noise more robustly.^[92] Counts per million (CPM) provides a simple scaling for comparative expression analysis.^[93] Batch effects from different runs or samples are corrected using algorithms like Harmony, which projects data into a shared low-dimensional space to align distributions without over-correcting biological signals.^[94] Popular tools for these steps include Seurat in R, which integrates QC, normalization via SCTransform, and batch correction in a modular workflow,^[48] and Scanpy in Python, offering efficient handling of large datasets with similar functionalities.^[95] As of 2025, Alevin-fry, an extension of the Salmon quantifier, enables rapid pseudoalignment and UMI deduplication for single-cell data, reducing processing time for massive datasets while maintaining accuracy.^[96]

Clustering and interpretation

After preprocessing, single-cell sequencing data undergoes dimensionality reduction to project high-dimensional gene expression profiles into lower-dimensional spaces, facilitating visualization and downstream analysis. Principal Component Analysis (PCA) is a linear method that captures the principal axes of variance, serving as an initial step in many workflows due to its computational efficiency and interpretability.^[97] Nonlinear techniques like t-distributed Stochastic Neighbor Embedding (t-SNE) emphasize local structure preservation for cluster visualization but can distort global relationships. Uniform Manifold Approximation and Projection (UMAP) improves upon t-SNE by better maintaining both local and global structures, often yielding more interpretable embeddings in single-cell RNA-seq datasets. Diffusion maps, which model data diffusion on a manifold, are particularly useful for inferring developmental trajectories by emphasizing temporal progression. Benchmarks across diverse datasets show UMAP and diffusion maps outperforming t-SNE in structure preservation, with adjusted Rand index (ARI) scores up to 0.75 for trajectory tasks.^[98] Clustering algorithms group cells into populations based on similarity in the reduced space, typically using graph-based approaches that construct a k-nearest neighbors (kNN) graph weighted by expression distances. The Louvain algorithm, implemented in the Seurat R package, optimizes modularity to detect communities, enabling scalable clustering of thousands of cells.^[99] The Leiden algorithm, available in the Scanpy Python toolkit, refines Louvain by ensuring better connectivity and resolution, reducing the risk of disconnected clusters.^[100] For simpler datasets, k-means clustering partitions cells into a predefined number of groups by minimizing intra-cluster variance, though it assumes spherical clusters and struggles with complex manifolds. The resolution parameter in graph-based methods controls cluster granularity; higher values yield finer partitions, tunable via silhouette scores or domain knowledge to balance over- and under-clustering.^[101] Recent benchmarks indicate graph-based methods like Leiden achieve ARI values of 0.80-0.90 on peripheral blood mononuclear cell datasets, outperforming k-means in hierarchical structures.^[102] Interpretation of clusters involves identifying biological significance through marker gene detection and functional annotation. The Wilcoxon rank-sum test compares gene expression distributions between clusters and the rest, flagging differentially expressed genes as markers; for instance, CD3D often marks T cells with log-fold changes exceeding 1.5 and adjusted p-values below 0.01.^[103] Pathway enrichment analysis, such as Gene Set Enrichment Analysis (GSEA), assesses coordinated changes in gene sets like immune response pathways, revealing upregulated signatures in specific clusters. Pseudotime inference orders cells along developmental trajectories; Monocle3 learns branched graphs via reversed graph embedding, while Slingshot fits principal curves to clusters for linear or diverging paths.^[104] These tools correlate pseudotime with gene expression gradients, identifying dynamic regulators like transcription factors in differentiation processes.^[105] In multi-omics contexts, integration methods jointly model modalities like RNA and protein data to enhance clustering robustness. MOFA+ performs unsupervised factor analysis with group-specific priors, decomposing variation into shared and modality-unique factors for cross-omics alignment. totalVI, a deep generative model, uses variational inference to integrate count-based data, accounting for technical noise and enabling probabilistic cell-type assignment. Benchmarks on datasets with RNA, ATAC, and protein profiles show these methods improving integration concordance, with normalized mutual information scores around 0.85 compared to unimodal approaches.^[106] Advanced machine learning tools like scVI leverage variational autoencoders (VAEs) for probabilistic modeling, imputation of dropout events, and batch correction, enhancing clustering accuracy by reconstructing latent spaces.^[107]

Applications in Biology and Medicine

Basic biological research

Single-cell sequencing has revolutionized basic biological research by enabling the dissection of cellular heterogeneity and dynamics at unprecedented resolution, revealing the intricate composition of tissues, developmental trajectories, and evolutionary processes that underpin life. This technology allows researchers to profile individual cells across diverse modalities, such as transcriptomics and genomics, providing insights into fundamental mechanisms without the averaging effects of bulk analyses. By capturing the diversity within cell populations, it facilitates the mapping of organ architectures, lineage commitments, microbial communities, mutational landscapes, and stress responses in non-model systems like plants. In tissue heterogeneity studies, single-cell sequencing has been instrumental in creating comprehensive atlases that catalog cell types and states across human organs, highlighting the diversity and shared features among cell populations. For instance, the Tabula Sapiens atlas profiles nearly 500,000 cells from 24 tissues and organs of multiple donors, identifying organ-specific variations in cell behaviors while revealing conserved transcriptional programs across cell types, such as T cell clonal sharing between immune-related organs. This resource underscores the mosaic-like structure of tissues, where rare subpopulations and transitional states contribute to overall function, advancing our understanding of multicellular organization.^[108] For developmental biology, single-cell sequencing integrates transcriptomic and epigenomic data to trace lineage specification during key events like gastrulation, elucidating how cells commit to embryonic fates. In human gastrulation, single-cell multi-omics approaches, such as scMAT-seq, have mapped epigenetic landscapes alongside gene expression, showing how chromatin accessibility and DNA methylation dynamically regulate lineage priming in epiblast cells transitioning to mesoderm, endoderm, and ectoderm progenitors. These profiles reveal principles of epigenetic memory and stochasticity in early development, providing a framework for modeling cell fate decisions.^[109] In microbial ecology, single-cell genomics has unlocked the genetic potential of uncultured bacteria, which constitute the vast majority of microbial diversity, by isolating and sequencing individual cells from environmental samples. This method bypasses cultivation biases, enabling the recovery of high-quality genomes from previously inaccessible taxa, such as rare gut symbionts or soil microbes, and revealing metabolic pathways like fiber degradation in human-associated bacteria. By profiling single cells, researchers can infer ecological roles and interactions in complex communities, transforming our view of microbial ecosystems. Single-cell sequencing also illuminates evolutionary dynamics within cell populations by quantifying mutation rates and phylogenetic relationships at the individual level, offering a window into neutral and adaptive processes. In somatic tissues, single-cell whole-genome sequencing reconstructs phylogenies that estimate mutation accumulation rates, demonstrating how proliferative dynamics influence genetic diversification independent of disease contexts. These analyses show that mutation rates vary with cell division history, providing quantitative measures of evolutionary tempo in healthy lineages. In plant biology, recent single-cell RNA sequencing efforts have exposed cellular heterogeneity in responses to environmental stresses like drought, identifying cell-type-specific regulatory networks that drive adaptation. A 2025 study on poplar trees used single-nucleus transcriptomics to profile xylem development under drought, revealing auxin-mediated arrest in cambial cells while other zones maintain proliferation, thus highlighting compartment-specific resilience mechanisms.^[110]

Clinical and translational applications

Single-cell sequencing has revolutionized clinical and translational applications by enabling precise characterization of cellular heterogeneity in diseases, facilitating earlier diagnosis, targeted therapies, and personalized medicine strategies. In oncology, it plays a pivotal role in dissecting tumor evolution and immune interactions, while in neurology and infectious diseases, it uncovers cellular mechanisms underlying pathogenesis and persistence. These insights have translated into clinical tools for monitoring treatment responses and identifying biomarkers, with ongoing advancements enhancing non-invasive detection methods. In cancer, single-cell DNA sequencing (scDNA-seq) has been instrumental in tracking subclonal evolution and drug resistance, particularly in hematological malignancies like acute myeloid leukemia (AML). For instance, high-throughput scDNA-seq of 123 AML patients revealed intricate clonal architectures and mutational histories, showing how resistant subclones emerge under therapeutic pressure and inform relapse prediction.^[111] Similarly, longitudinal single-cell profiling during chemotherapy in AML demonstrated that early treatment failure often stems from pre-existing resistant subclones, guiding adaptive dosing strategies to target these populations. Complementing this, single-cell RNA sequencing (scRNA-seq) identifies immunotherapy targets by mapping tumor-immune interactions; studies have used scRNA-seq to discover biomarkers predicting immune checkpoint blockade (ICB) responses, such as exhausted T-cell signatures in solid tumors, enabling patient stratification for therapies like PD-1 inhibitors. In neurology, single-nucleus RNA sequencing (snRNA-seq) has illuminated neuronal diversity in Alzheimer's disease (AD), revealing cell-type-specific vulnerabilities that drive progression. A comprehensive single-cell transcriptomic atlas of multiple brain regions from 283 post-mortem AD cases identified regionally distinct neuronal subtypes with altered amyloid and tau-related gene expression, highlighting excitatory neuron loss as a key pathological feature and potential therapeutic target. These findings support the development of disease-modifying drugs aimed at preserving specific neuronal populations, bridging basic heterogeneity insights to clinical trial design.^[112] For infectious diseases, single-cell multi-omics combining scDNA-seq and scRNA-seq has mapped viral reservoirs, exemplified by HIV persistence despite antiretroviral therapy. Integrated single-cell epigenetic, transcriptional, and protein profiling of latent HIV-1-infected cells uncovered heterogeneous states in CD4+ T cells, including transcriptionally active reservoirs that evade clearance, informing strategies like latency-reversing agents. In transplant medicine, single-cell sequencing monitors immune rejection by profiling T-cell states in allografts; scRNA-seq of renal biopsies delineated clonal CD8+ T-cell responses during acute cellular rejection, identifying effector and regulatory subsets that predict graft outcomes and enable immunosuppression tailoring. By 2025, multi-omics integrated into liquid biopsies has advanced early cancer detection with high sensitivity. Multi-omics models combining methylation and protein markers achieved 81.9% sensitivity for stage I-II gynecological cancers at 96.9% specificity, outperforming single-modality approaches.^[113]

Challenges and Future Directions

Current technical and computational challenges

Single-cell sequencing faces significant technical hurdles that limit its widespread adoption and accuracy. The high cost of conducting large-scale studies remains a major barrier, with comprehensive single-cell RNA sequencing (scRNA-seq) projects often requiring substantial funding in the millions of dollars depending on scale and modalities, primarily due to expensive reagents, instrumentation, and computational resources required for processing thousands to millions of cells.^[114] Cell dissociation from tissues frequently results in significant viability loss during enzymatic or mechanical processing, which introduces biases in transcriptional profiles and reduces the representation of fragile cell types such as neurons or endothelial cells.^[115] Additionally, many multi-omics approaches, which integrate transcriptomics with proteomics or epigenomics, suffer from low throughput, often capturing fewer than 10,000 cells per run due to technical constraints in simultaneous molecular capture and amplification, though high-throughput methods are emerging.^[116] Computationally, the vast dimensionality of single-cell datasets poses formidable challenges, as matrices comprising approximately 10,000 genes across 1 million cells can generate terabytes of raw data, necessitating advanced storage and processing infrastructure to handle sparsity and noise.^[117] Batch effects, arising from variations in experimental runs or protocols, can account for up to 30% of total variance in expression profiles, complicating the integration of datasets from different labs or time points and potentially masking true biological signals.^[118] Imputation methods to address dropout events—where genes are undetected due to low mRNA capture efficiency—often introduce inaccuracies; for instance, the Markov Affinity-based Graph Imputation of Cells (MAGIC) algorithm can add around 15% error in recovered expression values, distorting downstream analyses like trajectory inference.^[119] Standardization efforts are hindered by the absence of universal benchmarks, leading to reproducibility issues where coefficient of variation (CV) across laboratories exceeds 20% for key metrics such as gene expression levels in pseudo-bulk aggregates.^[120] Ethical concerns further complicate data handling, particularly privacy risks in large-scale human cell atlases, where linking attacks on count matrices can re-identify donors with high accuracy from seemingly anonymized public datasets.^[121] Bias in cell type annotation also persists, often stemming from reference dataset imbalances that favor abundant cell types and underrepresent rare or tissue-specific populations, resulting in misclassification rates of 10-30% in heterogeneous samples.^[122] As of 2025, the integration of spatial transcriptomics exacerbates data management challenges, with high-resolution imaging platforms generating terabytes of data per tissue slide due to the need to align millions of spatially resolved transcripts with imaging metadata.^[123] These volumes strain current computational pipelines, particularly for multi-modal spatial datasets that combine RNA with protein or DNA information.

Emerging technologies and perspectives

Recent advancements in long-read single-cell sequencing technologies, particularly those leveraging PacBio's single-molecule real-time (SMRT) sequencing, have significantly enhanced isoform resolution by capturing full-length transcripts averaging 1-2 kb, enabling the detection of complex alternative splicing events at the single-cell level.^[124] For instance, PacBio's Revio platform, with its high-throughput capacity of up to 480 Gb per day across four SMRT cells, supports the processing of approximately 1,000 cell lines in projects like the 1000 Genomes Long Read initiative, which uses Kinnex RNA kits to generate isoform data and address limitations in short-read methods for resolving transcript diversity.^[125] These developments, including techniques like HIT-scISO-seq and MAS-ISO-seq, concatenate multiple cDNAs for improved efficiency, paving the way for broader applications in dissecting cellular heterogeneity beyond current short-read constraints.^[124] In spatial omics, innovations such as MERFISH combined with sequencing enable high-plex in situ transcriptomics, achieving up to 500+ genes per experiment with subcellular resolution through error-robust fluorescence in situ hybridization on platforms like MERSCOPE.^[126] This approach measures RNA copy numbers in intact tissues, integrating sequential imaging and barcoding to profile large areas (up to 3 cm²) while maintaining compatibility with fixed samples like FFPE.^[126] Complementing this, NanoString's CosMx Spatial Molecular Imager supports whole-transcriptome analysis at single-cell and subcellular scales, with panels reaching 1,000-plex for targeted profiling of RNAs and proteins in the tumor microenvironment.^[127] These technologies overcome prior spatial limitations by providing multimodal data that links gene expression to tissue architecture, with demonstrated utility in immuno-oncology panels.^[128] Artificial intelligence and machine learning are transforming single-cell data analysis, with foundation models like scGPT pretrained on over 33 million cells to facilitate tasks such as denoising, cell type annotation, and predictive modeling of cellular trajectories.^[129] scGPT's generative architecture excels in perturbation response prediction and multi-omic integration, outperforming traditional methods in accuracy for downstream applications like gene network inference, though specific denoising benchmarks vary by dataset.^[129] Deep learning approaches, including autoencoders for noise reduction in scRNA-seq, achieve high fidelity in recovering true expression profiles, supporting trajectory inference that models dynamic processes like cell fate decisions.^[130] In vivo labeling techniques using CRISPR barcoding have advanced lineage tracing in animal models, introducing unique genetic mutations to track clonal histories alongside single-cell transcriptomics.^[131] Systems like dual-nuclease CRISPR-Cas9/Cas12a enable high-resolution recording of cell divisions and states in vivo, applied in mammals such as pigs and mice to reveal developmental hierarchies and tumor evolution.^[131] These methods surpass earlier retrospective tracing by integrating barcodes with scRNA-seq, providing simultaneous lineage and molecular snapshots in complex tissues.^[131] Looking ahead, single-cell sequencing is poised for routine clinical integration by 2030, driven by market expansion to $3.46 billion and increasing adoption in oncology and immunology for personalized diagnostics.^[132] Emerging wearables, such as CircTrek, enable real-time monitoring of circulating cells at single-cell resolution, hinting at future synergies with portable sequencing for dynamic health tracking.^[133] Additionally, initiatives like the Biodiversity Cell Atlas aim to create global single-cell maps for non-model organisms, standardizing methodologies to benchmark cellular diversity across species and inform evolutionary biology.^[134]

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Quality control (QC) in single-cell analysis removes low-quality cells using metrics like library size, expressed genes, and spike-in/mitochondrial proportions.1.2 Common Choices Of Qc... · 1.3. 2 With Adaptive... · 1.4 Checking Diagnostic...Missing: knee doublet Scrubblet
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Multiplexed bulk and single-cell RNA-seq hybrid enables cost ... - NIH
May 10, 2024 · Multiplexed coculture and demultiplexing natural genetic barcodes aid in studying genetic effects. Here, authors introduce Vireo-bulk to ...
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Multi-perspective quality control of Illumina RNA sequencing data ...
Sep 28, 2016 · The QC of RNA-seq can be divided into four related stages: (1) RNA quality, (2) raw read data (FASTQ), (3) alignment and (4) gene expression.Rna Quality · Raw Read Data Qc · Alignment Qc<|separator|>
[60]
Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human ...
Our study provides a useful framework for future investigation of human developmental hematopoiesis in the context of blood pathologies and regenerative ...
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Common Considerations for Quality Control Filters for Single Cell ...
Oct 27, 2022 · Here, we discuss the most common metrics and methods used for QC and filtering of cell barcodes in single cell RNA-seq data for gene expression analysis.Missing: knee | Show results with:knee
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Scrublet: Computational Identification of Cell Doublets in Single-Cell ...
Scrublet is a framework for predicting the impact of multiplets and identifying problematic multiplets in single-cell transcriptomic data.Missing: knee | Show results with:knee
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SoupX removes ambient RNA contamination from droplet-based ...
Dec 26, 2020 · We present SoupX, a tool for removing ambient RNA contamination from droplet-based single-cell RNA sequencing experiments.Soupx Removes Ambient Rna... · The Soupx Method · Application Of Soupx To Pbmc...Missing: subtraction | Show results with:subtraction
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Data normalization for addressing the challenges in the analysis of ...
May 6, 2024 · Normalization is a critical step in the analysis of single-cell RNA-sequencing (scRNA-seq) datasets. Its main goal is to make gene counts comparable within and ...<|separator|>
[65]
Alevin-fry unlocks rapid, accurate, and memory-frugal quantification ...
We have introduced alevin-fry as an accurate, computationally efficient, and lightweight framework for the processing of both single-cell and single-nucleus RNA ...
[66]
Accuracy, robustness and scalability of dimensionality reduction ...
Dec 10, 2019 · We compare 18 different dimensionality reduction methods on 30 publicly available scRNA-seq datasets that cover a range of sequencing techniques and sample ...
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A comparative study of manifold learning methods for scRNA-seq ...
Aug 7, 2025 · We compare four dimensionality reduction methods-PCA, t-SNE, UMAP, and Diffusion Maps-on three benchmark scRNA-seq datasets (PBMC3k, Pancreas, ...
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scanpy.tl.leiden - Read the Docs
resolution float (default: 1 ). A parameter value controlling the coarseness of the clustering. Higher values lead to more clusters. Set to None if overriding ...
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Optimization of clustering parameters for single-cell RNA analysis ...
The present study aimed to predict the accuracy of clustering methods when varying different parameters by exploiting the intrinsic goodness metrics.
[70]
[PDF] On the benchmarking of clustering algorithms and hyperparameter ...
Aug 25, 2025 · On the benchmarking of clustering algorithms and hyperparameter influence for cell type detection in single-cell RNA sequencing data. Aleksandra ...
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Differential gene expression - GitHub Pages
Mar 24, 2025 · In single cell, differential expresison can have multiple functionalities such as identifying marker genes for cell populations, as well as ...7 Compare Specific Clusters · 8 Dge Across Conditions · 8.3 Subsample<|separator|>
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Slingshot: cell lineage and pseudotime inference for single-cell ...
Jun 19, 2018 · We introduce Slingshot, a novel method for inferring cell lineages and pseudotimes from single-cell gene expression data.
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Trajectory-based differential expression analysis for single-cell ...
Mar 5, 2020 · We only consider Monocle 3 because it is the only method that provides a test of the association between gene expression and pseudotime within a ...
[74]
Multitask benchmarking of single-cell multimodal omics integration ...
Oct 13, 2025 · Here we develop a much-needed guideline on choosing the most appropriate method for single-cell multimodal omics data analysis through a ...
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Top 10 Bioinformatics Tools for scRNA-seq in 2025 - Neovarsity
May 16, 2025 · In this blog, we highlight 10 of the most impactful and widely adopted tools in single-cell analysis today.
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Overcoming barriers to single-cell RNA sequencing adoption in low
Apr 2, 2024 · Scientists in LMICs experience significant barriers to accessing sustainable funding for research, and the high costs of scRNAseq studies are ...
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Systematic assessment of tissue dissociation and storage biases in ...
Jun 2, 2020 · Single-cell RNA sequencing has been widely adopted to estimate the cellular composition of heterogeneous tissues and obtain transcriptional ...
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Single-Cell Multiomics Techniques: From Conception to Applications
This review summarizes recent progress in single-cell multiomics approaches, and focuses, in particular, on the most innovative techniques that integrate ...
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Single-cell Transcriptome Study as Big Data - ScienceDirect.com
Multi-institutional collaborative omics studies on the next-generation sequencing (NGS) platform have generated petabytes of data that constitute 'big data' ...
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CellMixS: quantifying and visualizing batch effects in single-cell ...
As shown in Fig 1A, batch effects attributed to sequencing protocols (cellbench, hca, pancreas) showed the highest average per cent variance explained by the ...
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Zero-preserving imputation of single-cell RNA-seq data - Nature
Jan 11, 2022 · MAGIC, SAVER, and DCA also improved the average error to 10.3%, 9.8 ... An accurate and robust imputation method scimpute for single-cell rna-seq ...
[82]
Precision and Accuracy in Quantitative Measurement of Gene ...
Apr 15, 2024 · Our analysis revealed that the median CV of detected genes across technical replicates based on pseudo-bulks was 0.68 ± 0.24 in the 14 brain ...
[83]
Private information leakage from single-cell count matrices
Oct 2, 2024 · Single-cell RNA sequencing can reveal private information through linking attacks. Individuals can be reidentified using publicly available data with or ...
[84]
A comparison of scRNA-seq annotation methods based on ...
Aug 9, 2024 · We believe that experimentally labeled single-cell immune cell-subtype datasets can avoid the computational biases of reference datasets caused ...Introduction · Methods · Results · Discussions and conclusions
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Stereo-seq V2: Spatial mapping of total RNA on FFPE sections with ...
Aug 28, 2025 · We demonstrated the robust performance of Stereo-seq V2 on clinical FFPE samples using triple-negative breast cancer (TNBC) sections and ...
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https://pmc.ncbi.nlm.nih.gov/articles/PMC11087505/
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PacBio Joins the 1000 Genomes Long Read Project to Add Isoform ...
Jul 23, 2025 · Sequencing is being carried out on 1,000 cell lines using PacBio's Kinnex RNA kits and Revio long-read platform, with each sample expected to ...Missing: cells | Show results with:cells
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MERFISH Spatial Transcriptomics - Vizgen
MERFISH is a massively multiplexed single-molecule imaging technology for spatially resolved transcriptomics capable of simultaneously measuring the copy number ...Missing: plex | Show results with:plex
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CosMx Spatial Molecular Imager - NanoString
Elevate your single-cell research with CosMx SMI. It provides multiomics insight into any sample type at cellular and subcellular resolution… CosMx® SMI Best ...CosMx® SMI · CosMx SMI Performance · CosMx Custom Solutions
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Comparison of imaging based single-cell resolution spatial ... - Nature
Sep 26, 2025 · A predesigned CosMx 1,000-plex panel, MERFISH 500-plex immuno-oncology panel, and Xenium 289-plex human lung panel were selected for this study.Missing: omics | Show results with:omics
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scGPT: toward building a foundation model for single-cell multi-omics using generative AI - Nature Methods
### Summary of scGPT Applications in Single-Cell Sequencing
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Deep learning in single-cell and spatial transcriptomics data analysis
Apr 4, 2025 · First, single-cell sequencing data are high-dimensional and sparse, and are often contaminated by noise and uncertainty, obscuring the ...
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Single-cell lineage tracing techniques in hematology
Mar 4, 2025 · This review focuses on the superiority of the emerging single-cell lineage tracing technologies of Integration barcodes, CRISPR barcoding, and base editors.
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Market Forecast News: Single Cell Sequencing Industry to Hit $3.46 ...
Aug 25, 2025 · Industry news: Single Cell Sequencing industry projected to reach $3.46B by 2030. Growing applications in oncology & immunology, ...
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A wearable device for continuous monitoring of circulating cells at ...
Mar 3, 2025 · We present CircTrek, a wearable device that for the first time enables continuous monitoring of circulating cells at single-cell resolution.Missing: sequencing | Show results with:sequencing
[96]
£3m funding for project to chart cellular diversity on Earth
Jan 9, 2024 · The funding will allow the group to test and benchmark methodologies for profiling single-cell atlases in non-model organisms. This will lay ...<|control11|><|separator|>