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You can request a service order and submit a quote in this page
Sample drop-off is located at the back entrance of the SeqMatic Laboratory (Suite # 120). Laboratory staff will receive your samples and provide signatures and receipt confirmations, just ring the doorbell. If in doubt, we can also help you at the front entrance.
The SeqMatic address is:
48383 Fremont Blvd., Ste. 120,
Fremont, CA 94538
If you have any questions, you can contact SeqMatic via email at: info@seqmatic.com
Or by calling: 1.510.870.0965
Yes, you need a PO before you submit your samples for processing.
The PO should reference a valid SeqMatic quote number. Credit Card purchases are also accepted; you can set this by submitting a service quote on the SeqMatic “Get a Quote” page.
Yes, the SeqMatic laboratory can extract and isolate DNA or RNA from any sample format. A variety of tissue samples and sample types, including from low to high throughput are accepted:
For Histology:
The list of accepted sample types is also available in the SeqMatic/extraction-services
No. The SeqMatic laboratory only accepts samples that are flash frozen or stored in RNALater.
Make sure to discuss your project with a SeqMatic scientist to determine the sample quantity required for processing.
SeqMatic is a CLIA/CAP accredited next generation sequencing (NGS) contract research organization based in Fremont, California. Founded in 2012 by former Illumina R&D scientists, SeqMatic provides end to end sequencing services including DNA sequencing, RNA sequencing, single cell RNA sequencing, epigenomics, spatial transcriptomics, histopathology, and bioinformatics analysis. SeqMatic is a Certified Service Provider for Illumina, 10x Genomics, and Parse Biosciences. The laboratory operates under CLIA and CAP quality standards, applying regulatory grade quality systems to all research and clinical projects.
SeqMatic offers a comprehensive range of NGS services:
DNA sequencing: whole genome sequencing (WGS), whole exome sequencing (WES), PCR amplicon sequencing, metagenomics, and non-model organism sequencing
RNA sequencing: bulk mRNA seq, bulk total RNA, miRNA and small RNA, FFPE RNA, and exosome sequencing
Single cell RNA sequencing on 10x Genomics Chromium, Parse Biosciences Evercode, and Scale Bio platforms, including gene expression, immune profiling, CITE seq, ATAC, Multiome, and methylation
Epigenomics: bulk ATAC seq, methylation (methyl seq), single cell ATAC seq, ChIP seq, and Multiome
Spatial transcriptomics: Visium and CytAssist
Histopathology: necropsy and grossing, tissue processing, embedding and sectioning, histological staining assays, whole slide imaging and analysis, and pathologist review
Pre-clinical and clinical laboratory services under CLIA/CAP accreditation
Bioinformatics analysis at primary, secondary, and tertiary tiers across all service types
SeqMatic also offers general services including nucleic acid extraction, pre-made library sequencing, project planning and consultation, and express turnaround options.
Yes. SeqMatic operates a CLIA licensed and CAP accredited laboratory. CLIA (Clinical Laboratory Improvement Amendments) and CAP (College of American Pathologists) accreditation means the laboratory meets federally mandated quality control, proficiency testing, and personnel standards. This accreditation applies to Laboratory Developed Tests (LDTs) and clinical projects performed at SeqMatic. CLIA/CAP accreditation does not apply to research use only (RUO) projects; however, SeqMatic follows CLIA quality standards throughout the laboratory, including RUO work. For researchers whose work may support IND filings or clinical translation, this means sequencing data is generated under regulatory grade quality systems from the start.
SeqMatic is located at 48383 Fremont Blvd., Ste. 120, Fremont, CA 94538. All sequencing is performed at this facility. SeqMatic does not subcontract work to third party or overseas laboratories.
SeqMatic accepts shipped samples from anywhere in the United States and internationally. SeqMatic holds import permits from the Centers for Disease Control (CDC) and the US Department of Agriculture (USDA), following all import compliance requirements. For Bay Area researchers, SeqMatic also offers local sample pickup services described in the FAQ below.
Submit a quote request through the SeqMatic website. A member of the technical team will follow up to discuss your project objectives, sample types, omics service of interest, platform options, sequencing requirements, and more. SeqMatic provides a scientific consultation for every project to help you select the right workflow, chemistry, and sequencing depth before any samples are committed.
Yes, for researchers in the San Francisco Bay Area. SeqMatic offers two local services not available from other CROs. For customers interested in single cell services, Onsite Seq brings a SeqMatic team member to your laboratory to perform cell fixation or GEM creation on location for any omics workflow, protecting cell viability for fresh samples.
Fetch Seq is a local courier pickup service that delivers your samples to SeqMatic, typically within 1 to 1.5 hours of pickup. Both services cover a 100 mile radius from Fremont, CA. Researchers outside the Bay Area can ship samples to SeqMatic from anywhere in the United States and internationally.
Yes. The BIOSECURE Act, enacted in December 2025 as part of the Fiscal Year 2026 National Defense Authorization Act, restricts US federal agencies, contractors, and grant recipients from using biotechnology equipment or services from designated biotechnology companies of concern, defined as entities owned or controlled by foreign adversary governments. SeqMatic is a US owned and operated, CLIA/CAP accredited laboratory in Fremont, California. All sequencing is performed in house in the United States, with no subcontracting to third party or overseas facilities. Researchers using federal grant or contract funding can work with SeqMatic without the supply chain restrictions the BIOSECURE Act is designed to address.
SeqMatic’s scientific work is led by a team with distinct areas of responsibility. Su Chen, MD, PhD, Medical Director, provides clinical oversight, interpretation, and clinical reporting, along with pathology reviews and histology expertise. Kelvin Chan, VP of Technology, focuses on operations, development, troubleshooting, customer consultations, new technologies, and bioinformatics. Ann Frazier, Associate Director of Clinical Laboratory, leads day to day laboratory operations and clinical workflows. Customers work directly with the scientists responsible for their projects, which is central to how SeqMatic maintains data quality. Kelvin also serves as the designated technical reviewer for SeqMatic’s published scientific content.
SeqMatic operates under documented quality management systems consistent with CLIA and CAP requirements. Every sample undergoes QC checks on receipt before library preparation and/or sequencing begins. Every library prepared in house is validated by MiSeq QC sequencing before committing to the production run, so library quality issues are caught before they consume reagent and instrument time. Sequencing performance is monitored against vendor yield specifications, which SeqMatic has historically outperformed across run types. SeqMatic does not mix samples from multiple customer projects in a single run, avoiding the risk of cross contamination and index (barcode) hopping. Bioinformatics outputs follow platform standard pipelines, with custom reference construction available for non-model organisms.
SeqMatic works with biotech and pharmaceutical companies, clinical laboratories, academic researchers and core facilities, agricultural and environmental research groups, government agencies, and other contract research organizations. Project scale spans single sample pilots through atlas scale studies. The lab handles traditional human and mouse (model) organisms and specializes in non-model organisms such as non-human primate, livestock, plant, marine, wildlife, domestic animals, and other unique species. CLIA/CAP accreditation means projects can begin under research use only and transition to clinical or regulated workflows in the same facility without changing service providers.
Yes. SeqMatic supports any or all segments of the omics workflow that best fits customer needs. For example, you can send blood, cells, or tissues that require extraction, purified DNA/RNA, or prepared libraries, and we will complete the workflow through sequencing. We also offer primary, secondary, and tertiary bioinformatics as needed.
SeqMatic is located in Fremont, California, and all work is performed in our Fremont laboratory. We do not outsource to third parties or send your samples overseas. For San Francisco Bay Area customers, SeqMatic offers a door to door courier pickup service called Fetch-Seq. A courier collects your samples as soon as they are ready and delivers them directly to the SeqMatic lab, typically within about an hour of pickup, so chain of custody can be tracked in real time from pickup to delivery. For customers running single cell workflows, where project success depends heavily on cell viability, SeqMatic offers Onsite-Seq: our scientists travel to your lab with all the equipment needed and can fix cells or perform GEM creation on site. Once the cells are stable, we hand carry them back to the SeqMatic lab to complete the single cell workflow.
Yes. SeqMatic operates a full service histopathology lab that accepts tissues either cryopreserved (snap frozen) for frozen processing or in formalin for FFPE processing. We can gross and trim tissues, process, embed, section, stain, digitally scan, and analyze tissues, including pathologist review. We offer a wide range of tissue staining including routine, special, immunohistochemistry (IHC), and histochemical stains. Histology for spatial transcriptomics is a particular strength, including custom tissue microarrays (TMAs) designed to allow more tissues per spatial slide, reducing the cost of spatial analysis per tissue.
The BIOSECURE Act, enacted in December 2025 as part of the Fiscal Year 2026 National Defense Authorization Act, restricts US federal agencies, contractors, and grant recipients from using biotechnology equipment or services from designated biotechnology companies of concern, defined as entities owned or controlled by foreign adversary governments. SeqMatic is a US owned and operated, CLIA certified laboratory in Fremont, California. All work is performed in house in the United States, with no subcontracting to third party or overseas facilities. SeqMatic’s US based operations align with the supply chain objectives the Act addresses. SeqMatic is also SOC 2 and HIPAA compliant.
SeqMatic accepts a wide range of sample types across all service categories. For DNA and RNA sequencing, the laboratory accepts extracted nucleic acids, tissue (animal and plant), cells, whole blood, plasma, serum, soil, fecal specimens, environmental samples, FFPE blocks and sections, and cryopreserved material. For single cell RNA sequencing, the laboratory accepts single cell suspensions,
intact tissues for dissociation, isolated nuclei, and fixed or frozen cells. SeqMatic specializes in the handling of low input, challenging, and degraded samples, and accepts samples at any stage of the sequencing workflow, from raw tissue through pre-made libraries ready for sequencing.
SeqMatic operates multiple sequencing platforms to match different throughput, read length, and cost requirements:
SeqMatic is a Certified Service Provider for Illumina.
For sequencing, most standard sequencing projects are completed within 1 to 2 weeks from sample receipt to data delivery. Express turnaround is available in as few as 3 to 5 days for sequencing services.
For workflows, projectsfollow separate turnaround timelines; see the relevant service pages for project specific estimates. Actual turnaround depends on sample complexity, the number of samples, sequencing depth, and bioinformatics scope.
Yes. SeqMatic has a full time in-house bioinformatics team that supports all service types, with a full suite of custom analytic pipelines that can be tailored to individual project needs, including support for non-model organisms. Available analyses include:
DNA: variant calling, allele frequency analysis, genome assembly, and insertion and deletion site mapping
RNA: differential expression analysis, pathway analysis, and alternative splicing
Single cell: Cell Ranger gene expression and immune profiling analysis
Spatial: Space Ranger for Visium spatial transcriptomics
De novo genome and transcriptome assembly
This list is not all inclusive. If your analyses of interest is not listed, contact SeqMatic to discuss feasibility.
Yes. If you prepare your own sequencing libraries, SeqMatic can perform QC, sequencing, and data analysis on pre-made libraries. This option is available across all sequencing platforms. SeqMatic validates every in-house prepared library via MiSeq QC sequencing before committing to the production run, and the same QC step is available for customer-prepared libraries.
Yes. SeqMatic provides histopathology services including necropsy and grossing, tissue processing, embedding and sectioning, histological staining assays ( routine stains (H&E), special stains (i.e.Trichrome, VVG, PAS), and advanced stains (IHC, IF)), and automated whole slide imaging, image analysis, as well as Pathologist review (California Board Certified Pathologist). These services can be performed as standalone assays or integrated with spatial transcriptomics (Visium, CytAssist) for combined morphological and gene expression profiling from the same tissue section.
The SeqMatic laboratory offers comprehensive full and partial services for:
The laboratory supports flexible operations with easy engagement at any workflow stage. Additionally, the laboratory specializes in the handling of low input, challenging and degraded samples.
Yes, the laboratory supports flexible operations with easy engagement at any workflow stage. Additionally, the laboratory specializes in the handling of low input, challenging and degraded samples.
Talk to one of our laboratory scientists, we can help optimize results to reach your goals within your required timeframe.
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Yes, the laboratory offers streamlined and highly customizable data solutions for primary, secondary and tertiary analysis.
Talk to one of our laboratory scientists, we can help optimize results to reach your goals within your required timeframe.
Standard single cell RNA sequencing projects at SeqMatic are completed in 3 to 6 weeks from sample receipt to data delivery. This includes sample QC, library preparation, sequencing, and primary data analysis. Expedited turnaround is available in as few as 2 weeks for time sensitive projects. Actual turnaround depends on sample quality, target cell number, sequencing depth, and the scope of bioinformatics analysis requested.
SeqMatic accepts single cell suspensions, intact tissues (which the team dissociates in house), isolated nuclei, and fixed or frozen samples. For 10x Genomics workflows, fresh or cryopreserved single cell suspensions with high viability (typically above 80%) produce the best results. For Parse Biosciences Evercode workflows, samples can be fixed using the Parse cell or nuclei fixation kit, enabling storage for up to 6 months and batch processing across time points. FFPE derived samples are supported through both Parse Evercode FFPE kits and 10x Genomics Flex Apex chemistry.
Yes. Single cell workflows for FFPE are available through 10x Genomics Flex Apex, which uses a probe-based assay on fixed cells and FFPE, and Parse Biosciences, which offers instrument-free processing of fixed samples. Parse Evercode remains differentiated by its full length transcript coverage, species agnostic chemistry, scale (up to 5 million cells per kit), and the combinatorial barcoding approach that does not require any specialized instrument. For researchers choosing between these options, see the platform comparison FAQ above.
SeqMatic supports single cell RNA sequencing for human, mouse, and a wide range of non-model organisms. SeqMatic has successfully processed single cell RNA workflows for non-model organisms including crops, marine life, livestock, and wildlife. Species processed at the SeqMatic laboratory include: rat, chicken, cattle, pig, horse, dog, squirrel, non-human primates (NHP), soybeans, cotton, tomato, potato, wheat, grape, banana slugs, salmon, and catfish.
Most single cell kits are designed for human and mouse. SeqMatic has adapted these workflows for non-model organisms and can build custom reference genomes for species with incomplete or poorly annotated transcriptomes.
The decision depends on your sample type, throughput needs, and experimental goals.
Choose 10x Genomics Chromium if you are working with fresh or cryopreserved single cell suspensions, need multi-omic readouts (gene expression plus surface protein, ATAC, or immune profiling), or want paired BCR/TCR repertoire analysis alongside transcriptome data. 10x Genomics has the largest ecosystem of downstream analysis tools and the most extensive published benchmarking data.
Choose 10x Genomics Flex Apex if your samples are fixed, frozen, or FFPE and you want to stay within the 10x Genomics ecosystem. Flex Apex uses a probe-based assay that works on fixed cells and supports multiplexing up to 384 samples per run.
Choose Scale Bio if you need single cell DNA methylation profiling. Its Single Cell Methylation kit is the only commercially available single cell methylation assay, and is not offered through standard 10x Chromium or Parse Biosciences workflows.
Choose Parse Biosciences Evercode if you need instrument-free processing, are profiling more than 100,000 cells, are batching samples collected at different times or sites, or are working with non-model organisms where full length transcript coverage improves gene quantification against draft or incomplete reference annotations. Parse Evercode sequences across the entire transcript, enabling improved isoform detection and greater tolerance of poorly annotated genomes. Because the technology is instrument-free, it is also better suited for fragile, archived, field-collected, or hard-to-dissociate tissues where cell clumping or debris could clog droplet-based microfluidics.
SeqMatic is certified for both 10x Genomics and Parse Biosciences and can help you select the right platform during the project consultation step. In cases where the choice is not clear cut, the team can design a pilot experiment on both platforms to compare results before committing to a full-scale run.
Recommended cell input depends on the platform, sample type, kit choice, and cell viability.
For tissues, samples can be submitted as fresh tissue preserved in storage media or cryopreserved. For fresh tissue, SeqMatic recommends 50 mg of tissue per sample for optimal cell recovery. For cryopreserved tissues, nuclei are isolated (since viability from cryopreserved tissue is low), and a minimum of 50 mg per sample is recommended for optimal nuclei recovery.
For cells, samples can be submitted as viable cell suspensions in growth media or cryopreserved. For fresh suspensions, submit 2x to 3x the targeted number of viable cells per sample. For cryopreserved cells, submit a minimum of 1 million cells per sample.
For 10x Genomics Chromium, a typical target is 500 to 20,000 cells per channel, with a recommended minimum viability of 80%. Submit at least 2x the target number of viable cells to account for processing losses.
For Parse Biosciences Evercode, cell input is flexible across kits: the WT Mini kit supports as few as 10,000 cells, while the WT Penta kit scales to 5 million cells.
SeqMatic scientists help you determine the optimal cell input based on your target cell population, expected recovery rate, and downstream analysis goals.
Recommended sequencing depth varies by library type. General targets for the most common library types:
Gene Expression (10x 3′ or 5′, Parse WT): 20,000 to 50,000 reads per cell
ATAC: 25,000–50,000 read pairs per nucleus
V(D)J: 5,000 reads per cell
Flex Apex: 10,000 reads per cell
Feature Barcoding / CITE-seq: 5,000 reads per cell
Yes. SeqMatic offers bioinformatics analysis at three tiers:
Primary. Cell Ranger (10x) or Split-pipe (Parse) processes single cell data by barcode demultiplexing, read alignment, and construction of single cell expression count matrices. Deliverables include web summary reports, a gene–cell expression matrix, and aligned BAM files.
Secondary. Downstream analysis where the expression count matrix is subjected to quality control, normalization, and filtering to remove low quality cells and technical artifacts. Deliverables include a QC filtered expression matrix, a cell level QC metrics table, a normalized expression matrix, and QC reports and plots.
Tertiary. Interpretation of the biological structure of the data through dimensionality reduction, clustering, and cell type annotation using tools such as Seurat or Scanpy. Deliverables include a processed AnnData object, cluster annotations with assigned cell types, dot plots and violin plots of marker genes, and differential gene expression (DGE) results for each cluster or cell type.
Yes. SeqMatic offers two services designed to preserve sample quality for Bay Area researchers.
Onsite-Seq brings a SeqMatic team member to your lab to perform cell fixation or GEM creation on site, protecting cell viability and avoiding cell decay in transit. Fetch-Seq is a dedicated, door to door sample pickup service that delivers samples directly to SeqMatic, typically within 1 to 1.5 hours of pickup depending on location. It is a personalized pickup, not a shared route with fixed stops.
Both services are available to researchers in the San Francisco Bay Area and cover a 100 mile radius from Fremont, CA. Fetch-Seq is priced at a flat fee. Onsite-Seq is priced per visit.
These services exist because cell viability is the single largest determinant of data quality in fresh sample single cell workflows. Reducing transit time from lab bench to SeqMatic’s processing facility preserves viability and increases the percentage of high-quality cells captured in the final dataset.
The cost of a single cell RNA sequencing project depends on several factors, and SeqMatic provides customized quotes based on each study’s requirements. The primary variables that affect pricing are the number of samples, the number of cells per sample, the platform (10x Genomics, Parse Biosciences, or Scale Bio), the library type (standard gene expression, immune profiling, ATAC, Multiome, CITE seq, or methylation), the sequencing depth per cell, and the scope of bioinformatics analysis.
Projects with higher cell counts require proportionally more sequencing, which increases the sequencing component of the total cost. Parse Biosciences Evercode tends to be more cost-effective at high cell counts (above 100,000) because the Evercode chemistry scales without additional instrument runs. 10x Genomics Chromium may be more cost-effective for smaller experiments with multi-omic readouts. Scale Bio kits offer a middle path for high throughput instrument-free processing within the 10x ecosystem.
SeqMatic scientists work with you during the project consultation step to design an experiment that balances scientific goals with budget, and can recommend adjustments to cell count, sequencing depth, or platform selection to optimize cost.
Single cell RNA sequencing (scRNA seq) profiles the transcriptome of intact whole cells, capturing both cytoplasmic and nuclear RNA. Single nuclei RNA sequencing (snRNA seq) profiles the transcriptome of isolated nuclei rather than whole cells, capturing nuclear RNA including pre mRNA and mature transcripts that are present in the nucleus at the time of isolation.
The choice between the two depends on the sample type and the biology you are studying. Whole cell scRNA seq is the standard approach when you can obtain a high viability single cell suspension from fresh or cryopreserved tissue. It generally detects more genes per cell because cytoplasmic mRNA is included. snRNA seq is the better option when intact cells cannot be recovered, which is common with frozen tissues, archived specimens, cell types that are too large or fragile to survive dissociation (such as adipocytes, cardiomyocytes, or neurons), and samples where enzymatic dissociation would alter gene expression profiles.
Both approaches are supported at SeqMatic. 10x Genomics Chromium supports nuclei for Universal Gene Expression, Flex Apex, ATAC seq, and Multiome workflows. Parse Biosciences Evercode supports nuclei through fixation, and because Evercode does not require microfluidics, it handles nuclei from difficult to dissociate tissues without the viability constraints that affect whole cell droplet-based workflows. SeqMatic scientists can help you determine which approach is appropriate for your sample type during the project consultation step.
Yes. Long read single cell sequencing is ideal if your study requires full length transcript discovery, precise isoform quantification, structural variant or fusion detection, or allele specific or haplotype resolved analysis.
If your primary goal is large scale cell clustering or gene expression quantification, short read single cell RNA seq may be more cost-effective. Many projects benefit from a hybrid strategy combining both technologies. Contact SeqMatic for details.
Yes. SeqMatic accepts cryopreserved single cell suspensions for all standard 10x Genomics workflows (Universal 3′ GEx, Universal 5′ GEx, immune profiling, Feature Barcoding). Cells should be cryopreserved using a validated protocol with a controlled rate freezer or isopropanol-based container, stored in liquid nitrogen, and shipped on dry ice. Upon receipt, SeqMatic performs viability assessment after thawing. Recovery rates from cryopreserved samples are typically 60 to 90% of the pre-freeze count, depending on cell type and cryopreservation method. For best results, submit samples with a pre-freeze viability above 90%.
Choosing the proper preservation chemistry is critical to project success. SeqMatic has experience with numerous preservation reagents and can recommend the best chemistry for your specific tissue type. Recommended protocols are provided during technical discussion with the SeqMatic scientific team. For additional reference, see the 10x Genomics knowledge base article on cell shipping.
SeqMatic performs viability assessment upon sample receipt. If viability falls below 80%, the team contacts you to discuss three options: proceed with the understanding that data quality may be reduced (higher ambient RNA contamination, lower per cell gene detection), decline to proceed and return the sample, or switch to the single nuclei RNA seq workflow, which eliminates viability requirements by profiling isolated nuclei instead of intact cells. The decision depends on the specific sample, experimental goals, and acceptable tradeoffs. For samples with consistently low viability, the Flex Apex (Fixed RNA Profiling) assay is another alternative that eliminates viability constraints entirely by fixing cells before processing.
The Chromium X supports loading 500 to 20,000 cells per channel with the standard single cell kit. Cell recovery rates are typically 50 to 65% of the loaded cell count, meaning a 10,000 cell loading target will yield approximately 5,000 to 6,500 recovered cells in the final dataset. The Flex Apex assay supports up to 1 million cells per GEM well and up to 384 samples in 96 well format. Scale Bio QuantumScale kits support up to 4 million cells per plate for instrument-free workflows.
SeqMatic sequences 10x Genomics libraries on Illumina NovaSeq X Plus, NextSeq, and Ultima Genomics UG100 platforms. The platform is selected based on the number of libraries, total cell count, required sequencing depth, and read configuration. NovaSeq X Plus and UG100 are used for higher throughput projects, while NextSeq is used for smaller experiments or rapid turnaround runs. All platforms produce data compatible with the Cell Ranger analysis pipeline.
Yes. SeqMatic supports Feature Barcoding for surface protein measurement alongside gene expression using antibody derived tags (ADTs). CITE seq is the most common Feature Barcoding application and enables simultaneous transcriptomic and proteomic profiling from the same cell. Researchers can supply their own oligo conjugated antibody panels or work with SeqMatic to select panels. Key vendors include BioLegend (TotalSeq A, B, and C), Abcam (validated for 5′ immune profiling with Lightning-Link conjugation), Proteintech Genomics (MultiPro panels for Chromium Flex), and Bio-Rad (conjugated antibodies for multiplexed surface analysis). Panels are ordered as needed for each project. Feature Barcoding can be combined with Cell Hashing for sample multiplexing within the same run.
SeqMatic offers bioinformatics analysis at three tiers for 10x Genomics data:
Primary — using Cell Ranger. Raw sequencing reads are processed and converted into a structured gene cell expression matrix through barcode demultiplexing, read alignment, and count matrix construction. Deliverables include web summary reports, a gene–cell expression matrix, and aligned BAM files. For Multiome data, Cell Ranger ARC is used.
Secondary — downstream analysis where the resulting expression count matrix is subjected to quality control, normalization, and filtering to remove low quality cells and technical artifacts. Deliverables include a QC filtered expression matrix, a cell level QC metrics table, a normalized expression matrix, and QC reports and plots.
Tertiary — interpretation of the biological structure of the data by performing dimensionality reduction, clustering, and cell type annotation using tools such as Seurat or Scanpy. Deliverables include a processed AnnData object, cluster annotations with assigned cell types, dot plots and violin plots of marker genes, and differential gene expression (DGE) results for each cluster or cell type.
Standard turnaround for 10x Genomics single cell projects at SeqMatic is 3 to 6 weeks from sample receipt to data delivery. This includes sample QC, library preparation, sequencing, and primary data analysis with Cell Ranger. Expedited turnaround is available in as few as 2 weeks for time sensitive projects. Actual turnaround depends on sample quality, number of libraries, sequencing depth, and bioinformatics scope.
The 3′ and 5′ designations refer to which end of the mRNA transcript is captured and sequenced. In the Universal 3′ assay, polyadenylated transcripts are captured from the 3′ (poly A tail) end. In the Universal 5′ assay, transcripts are captured from the 5′ end.
For most standard gene expression profiling experiments (cell type identification, differential expression, clustering), the Universal 3′ assay is the default choice. It is more widely used, has more published benchmarking data, and is generally sufficient for transcriptomic characterization.
The Universal 5′ assay is required when you need paired immune receptor sequencing. V(D)J libraries for BCR and TCR repertoire analysis can only be generated from 5′ gene expression captures because the variable regions of immune receptors are located at the 5′ end of the transcript. SeqMatic supports both chemistries. The general rule: if you need V(D)J or plan to add immune profiling later, start with 5′. If you do not need immune receptor sequences, 3′ is the standard recommendation.
Yes. The 10x Genomics Single Cell Epi Multiome assay captures both ATAC seq (chromatin accessibility) and gene expression from the same nucleus in a single workflow. This links epigenomic state to transcriptomic output at single cell resolution. Multiome uses isolated nuclei, so it is compatible with frozen tissues and samples where intact cells cannot be recovered. Primary analysis uses Cell Ranger ARC, and downstream integration can be done using Signac, ArchR, or Seurat.
SeqMatic handles the full Multiome workflow from nuclei isolation through sequencing and primary analysis. Because Multiome requires higher sequencing depth than standard gene expression (approximately 20,000 reads per nucleus for GEx and 25,000 read pairs per nucleus for ATAC), SeqMatic configures the sequencing run to meet both targets in a single run.
Yes. Researchers can fix cells at their own lab using the Parse Biosciences fixation kit (purchased directly from Parse Biosciences). Fixed cells are stable for up to six months, so shipping timelines are not a constraint. Fixed samples are shipped on dry ice. SeqMatic can accept cells fixed with non-Parse protocols but does not recommend them, as non-Parse protocols are not supported by Parse Biosciences. This makes Parse Biosciences Evercode accessible to labs anywhere in the country, regardless of proximity to SeqMatic’s Fremont facility.
Evercode whole transcriptome kits are species agnostic. Any organism with an available reference transcriptome can be processed, including non-model organisms. SeqMatic has processed single cell and single nuclei samples from human, mouse, and a wide range of additional species on the Parse platform, including crops, marine life, livestock, and wildlife. The species list above is not all inclusive. If your species of interest is not listed, contact SeqMatic to discuss feasibility. BCR and TCR immune repertoire kits are currently available for human and mouse only.
For non-model organisms, Parse Evercode offers an advantage over 3′ end capture platforms: because Evercode sequences across the entire transcript, it provides greater tolerance of incomplete or poorly annotated reference genomes and enables more robust gene quantification even when annotations are imperfect. SeqMatic also builds custom reference genomes and functional annotations for species without existing references.
The Evercode WT Mini kit supports as few as 10,000 cells, making it the most flexible option for pilot studies. There is no strict lower limit on cell input; however, very low cell counts may result in reduced gene detection per cell and higher per cell sequencing costs because the same library preparation and sequencing resources are applied to fewer cells. SeqMatic scientists can help you evaluate which Parse kit is the best solution.
Yes. This is one of the primary advantages of the Evercode fixation workflow. Samples collected days, weeks, or even months apart can be fixed at the point of collection and stored until all samples are ready for processing. All fixed samples are then pooled into a single split and pool run, which means every sample goes through identical processing conditions. This eliminates batch effects that arise when samples are processed in separate runs on different days. For time course studies, multi-site collaborations, and longitudinal experiments, this is a significant advantage over fresh sample workflows where each collection point introduces a new processing batch.
Yes. Formalin fixed paraffin embedded (FFPE) tissue sections are compatible with the Parse Biosciences Evercode workflow through the dedicated FFPE kit variants (WT FFPE Mini, WT, Mega, and Penta). Because Evercode uses fixed, permeabilized cells as the reaction compartment, the chemistry is inherently compatible with samples that have already been fixed.
For FFPE processing, tissue sections are deparaffinized, rehydrated, and dissociated into single nuclei or single cells before entering the Evercode split and pool barcoding pipeline. The quality of the resulting data depends on the fixation and storage conditions of the FFPE block: recently prepared blocks with shorter fixation times tend to produce better results than blocks that have been in storage for many years or were overfixed. SeqMatic performs quality assessment on FFPE derived samples upon receipt and can advise on whether the sample quality is sufficient for single cell resolution data before committing to a full library preparation.
Note: 10x Genomics Flex Apex also supports FFPE samples through a probe based approach. The choice between Parse FFPE and Flex Apex depends on whether you need full length transcript coverage and species agnostic chemistry (Parse) or 10x ecosystem compatibility and large scale sample multiplexing (Flex Apex). SeqMatic can advise on which approach is best for your specific FFPE samples.
Yes. SeqMatic offers bioinformatics analysis at three tiers for Parse Biosciences data:
Primary — using Split-pipe. Raw sequencing reads are processed and converted into a structured gene cell expression matrix through barcode demultiplexing, read alignment, and count matrix construction. Deliverables include web summary reports, a gene–cell expression matrix, and aligned BAM files.
Secondary — downstream analysis where the resulting expression count matrix is subjected to quality control, normalization, and filtering to remove low quality cells and technical artifacts. Deliverables include a QC filtered expression matrix, a cell level QC metrics table, a normalized expression matrix, and QC reports and plots.
Tertiary — interpretation of the biological structure of the data by performing dimensionality reduction, clustering, and cell type annotation using tools such as Seurat or Scanpy. Deliverables include a processed AnnData object, cluster annotations with assigned cell types, dot plots and violin plots of marker genes, and differential gene expression (DGE) results for each cluster or cell type.
Standard turnaround for Parse Biosciences projects is 3 to 6 weeks from sample receipt to data delivery. This includes sample QC, split and pool barcoding, library preparation, sequencing, and primary data analysis. Expedited turnaround is available in as few as 2 weeks. For large scale studies using the WT Mega or WT Penta kits, turnaround may extend depending on the total number of cells and required sequencing depth.
RNA sequencing measures gene expression averaged across all the cells in a sample, producing one expression profile per sample. Single cell RNA sequencing measures expression in individual cells, resolving cell type composition and rare populations that an average cannot show. RNA-seq is the right choice for population level comparisons, limited or degraded input material, and high throughput studies; single cell RNA-seq is the right choice when cellular heterogeneity drives the question. Many studies use both.
Choose total RNA-seq with ribosomal depletion when poly-A selected mRNA-seq would miss the transcripts you need. It is preferred for whole blood, cells such as bacteria, and tissues such as spleen, where poly-A mRNA is unavailable or overwhelmed by globin RNAs, and it is often the better option for poor quality or degraded samples such as FFPE. Total RNA-seq retains coding plus non-coding, structural, small, and miRNA transcripts. Choose mRNA-seq when your focus is protein coding gene expression and your RNA is intact.
Input requirements depend on the library type; see the four sample requirement tables above for recommended and minimum values. As a general guide, standard mRNA-seq recommends 1 µg of total RNA, and SeqMatic’s low input and small RNA workflows accept far less. If you cannot meet the minimum for your library type, discuss it with a SeqMatic scientist before submission, since lower input is often feasible.
SeqMatic qualifies each submitted RNA sample on a TapeStation electropherogram, which reports RIN and DV200. Recommended and minimum RIN and DV200 values by library type are given in the sample requirement tables above. Results are shared with the customer for review and approval before library preparation proceeds, and if a sample falls below requirements the team consults on how best to proceed rather than failing it automatically.
Yes. SeqMatic provides bulk total RNA sequencing from FFPE material. The recommended FFPE library preparation is the Watchmaker Genomics RNA Library Prep with Polaris Depletion, which combines ribosomal and globin depletion with a dedicated FFPE treatment step to recover signal from degraded, cross-linked RNA, with inputs from 1 ng to 1,000 ng. Recommended depth for FFPE bulk total RNA-seq is 50 to 100 million reads per sample. RNA quality is assessed by TapeStation before library preparation, and a full service histopathology laboratory is available to section FFPE blocks. Single cell and spatial FFPE profiling are covered on the single cell RNA sequencing page.
SeqMatic recommends 25 to 30 million reads per sample for standard mRNA-seq and 50 to 60 million for total RNA-seq, 50 to 100 million for FFPE bulk total RNA-seq, 30 million for exosome RNA-seq, 10 million for small RNA / miRNA, and 2 to 10 million reads for 3′ RNA screening. These figures apply to model organisms such as human and mouse; other species may differ, and higher or lower depths are available depending on project needs.
As a guide: choose Bulk mRNA-Seq for protein coding gene expression from intact RNA; choose Bulk Total RNA / Non-coding RNA for whole blood, bacterial, degraded, or FFPE samples, or when you need non-coding RNA coverage; choose miRNA & Small RNA for microRNA and other small non-coding RNA; choose FFPE RNA for archival tissue; choose Exosome for RNA cargo from biofluids; and consider 3′ RNA sequencing for large screens across many samples. SeqMatic’s team helps confirm the right package during the project consultation.
Yes. SeqMatic provides custom bioinformatics at three tiers — Primary (alignment and quantification), Secondary (QC, normalization, and differential expression), and Tertiary (pathway, gene ontology, and functional interpretation) — and can go deeper per customer request, including support for non-model organisms.
A laboratory services partnership provides the clinical laboratory expertise, regulatory infrastructure, sequencing workflows, bioinformatics, and reporting required to support regulated NGS programs from assay validation through patient testing.
A laboratory services partnership at SeqMatic is a structured engagement in which SeqMatic provides NGS workflow services, full or partial, for a sponsor’s clinical, translational, or regulated program. SeqMatic is a CLIA certified, CAP accredited omics services laboratory in Fremont, California. Clinical partnerships include LDT validation, companion diagnostic (CDx) development, clinical trial sequencing, and assay development and optimization.
Scope ranges from a single workflow component (sequencing only) to full onboarding and validation, including accessioning, biobanking, extraction, library preparation, sequencing, bioinformatics, Medical Director review, and clinical reporting.
CLIA certification is the federal requirement, administered by the Centers for Medicare and Medicaid Services (CMS), that a laboratory must meet to perform clinical testing on human samples in the United States. CAP accreditation is a rigorous peer inspection program from the College of American Pathologists that CMS recognizes as meeting or exceeding CLIA requirements. SeqMatic holds both, so testing is performed under federal quality standards and independently inspected against them.
A Laboratory Developed Test is developed when no suitable FDA cleared or approved test exists for a given intended use, or when a laboratory needs a test tailored to a specific sample type, biomarker, or patient population. The LDT is designed, validated, and used within a single CLIA certified laboratory under Medical Director oversight.
Yes. Assay transfer is the first stage of the validation workflow. SeqMatic onboards your NGS assay, trains the clinical team, performs workflow optimization, and demonstrates equivalent or better performance in our laboratory before the assay enters validation and routine use.
A Laboratory Developed Test is designed, developed, and executed within a single CLIA certified laboratory. Yes, SeqMatic validates LDTs that use NGS readouts. The workflow covers onboarding, feasibility, CLIA analytical validation across nine parameters (accuracy, precision, analytical sensitivity, analytical specificity, reportable range, reference interval where appropriate, limit of detection, reproducibility, and robustness), Medical Director approval, clinical reporting, documentation, training and competency, and CLIA/CAP inspection readiness.
SeqMatic performs clinical NGS on its qualified Illumina portfolio: NovaSeq X Plus, NovaSeq 6000, NextSeq, and MiSeq. Platform and read configuration are matched to the assay during onboarding.
Yes. SeqMatic offers wet lab only engagements that deliver FASTQ files, and full wet and dry lab engagements that add primary, secondary, and tertiary bioinformatics analysis, Medical Director review, and a clinical report. The dry lab work is handled by a full time in-house bioinformatics team.
Yes. The BIOSECURE Act addresses concerns that sensitive US genomic, health, and other biological data could be accessed or exploited through biotechnology companies viewed as posing national security risks. It restricts US federal agencies, contractors, and grant recipients from using biotechnology equipment or services from designated biotechnology companies of concern. SeqMatic is a US owned and operated, CLIA certified laboratory in Fremont, California, performing all work in house with no overseas subcontracting. SeqMatic’s US based operations align with the supply chain objectives the Act addresses.
Yes. SeqMatic maintains applicable CDC import permits for eligible biospecimens when required, and routinely receives clinical samples from global collection sites. All samples are accessioned and tracked in the SeqMatic LIMS, batched for efficient processing, and data is delivered securely through a client portal.
SeqMatic supports the laboratory components of companion diagnostic programs, including analytical validation, documentation, and the data packages used during FDA submission planning. The sponsor leads the regulatory submission; SeqMatic provides the clinical laboratory work and validation data that support it.
SeqMatic accepts extracted nucleic acids, whole blood, plasma, serum, fresh and cryopreserved tissue, FFPE blocks and sections, and pre-made sequencing libraries. The laboratory has specific expertise with low input, degraded, and FFPE material. Accepted sample types are confirmed during the project consultation step.
Turnaround depends on the engagement scope and the validation requirements of the assay, and is defined per project during consultation. SeqMatic supports batch sizes from a few samples using manual workflows to hundreds using automated instruments, and targets fast turnaround without compromising quality.
All data, results, algorithms, and documentation generated under contract are the exclusive property of the client and are not used or disclosed without prior written consent. Data is protected through SOC 2 Type 2 and HIPAA aligned controls, encryption at rest and in transit, role based access, and audit logging, and is delivered through a secure client portal.
The SeqMatic address is:
SeqMatic
48383 Fremont Blvd., Ste. 120,
Fremont, CA 94538
You can contact SeqMatic via email at: info@seqmatic.com
Or by calling: 1.510.870.0965
Other SeqMatic location and contact information is available in the SeqMatic/location page.
To reach the SeqMatic Laboratory at 48383 Fremont Blvd., Ste. 120, Fremont, CA 94538 from:
NORTH
From northern locations (such as Napa, Concord or Walnut Creek), the most direct route typically involves using I-680 South.
Driving Directions from the North
Alternative Route (Via I-880)
If traveling from Oakland or San Leandro:
Location Details
SOUTH
From southern locations like San Jose or Milpitas, the most efficient route is via I-880 North.
Driving Directions from the South
Alternative Route (Via I-680)
If you are coming from the East San Jose area:
Public Transit Options
EAST
From eastern locations such as Pleasanton, Sunol, or Livermore, the most efficient route is via I-680 South.
Driving Directions from the East
Alternative Route (Via Niles Canyon)
If traveling from the Sunol area and avoiding the highway:
WEST
From western locations like Menlo Park, Palo Alto, or Redwood City, the most direct route involves crossing the Dumbarton Bridge (CA-84 E).
Driving Directions from the West
Alternative Route (Via CA-237)
If you are coming from Mountain View or Sunnyvale:
Other SeqMatic location and contact information is available in the SeqMatic/location page.
The SeqMatic laboratory standard hours of operations are:
Other SeqMatic location and contact information is available in the SeqMatic/location page.
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