Enabling multiparameter profiling of precious samples, mass cytometry has been instrumental in achieving new research breakthroughs in areas such as immunology, cancer immunotherapy, drug discovery, vaccine development and more around the world.

Watch the webinars below to learn how researchers are utilizing Helios™, a CyTOF system, and mass cytometry applications to further their research.

	Finding Pathologic T Cells in Rheumatoid Arthritis by Mass Cytometry Deepak Rao, MD, PhD  Rheumatologist Co-Director, Human Immunology Center Brigham and Women's Hospital Watch
	Querying Cytokine-Signaling Networks in Myeloproliferative Neoplasms Stephen Oh, MD, PhD  Assistant Professor of Medicine, Division of Hematology  Washington University School of Medicine  Watch
	Enhancing Checkpoint Blockade in Lymphoma with In Situ Vaccination Joshua Brody, MD  Assistant Professor, Hematology and Medical Oncology Director, Lymphoma Immunotherapy Program Icahn School of Medicine at Mount Sinai Watch
	Decoding Tumors with Mass Cytometry Jonathan Irish, PhD Assistant Professor of Cancer Biology, Assistant Professor of Pathology, Microbiology and Immunology Vanderbilt University Watch
	Defining the Phenotypic and Functional Immune Microenvironment in AML Evan Lind, PhD Assistant Professor, Department of Molecular Microbiology and Immunology and Department of Cell, Development and Cancer Biology Oregon Health & Science University Watch
	Towards an Assay of Global Immune Competence Holden Maecker, PhD Associate Professor (Research) of Microbiology and Director, Human Immune Monitoring Center Stanford University Watch
	Signatures of Protective NK Cell Responses Catherine Blish, MD, PhD Assistant Professor, Department of Medicine and Immunology, Stanford University School of Medicine Assistant Director of the Stanford Medical Scientist Training Program Watch

For Research Use Only. Not for use in diagnostic procedures.

The C1™ system provides the widest range of automated single-cell applications in the industry, from gene expression profiling to genomic and epigenetic analysis. With more than 150 peer-reviewed publications, the C1 system has empowered significant research breakthroughs in the understanding of cell diversity and function in cancer, neurology, immunology and cardiovascular and stem cell biology.

The key to successful single-cell studies is preparing high-quality suspensions with maximum cell viability and minimum cell stress and debris. Whether you are working with cultured cells or with samples freshly isolated from tissue, cell quality is a critical factor for ensuring optimal results in single-cell datasets.

Now you can load enriched cell populations obtained by flow cytometric cell sorting directly into the C1 IFC (integrated fluidic circuit) to obtain rare subpopulations of cells with high purity and viability.

Benefits of this new application include:

•	A streamlined workflow that’s gentler and reduces cell losses as compared to sorting into a microfuge tube and then transferring to C1.
•	Reduced sample processing time.
•	Improved capture efficiency for neurons and immune cells.

To learn more, download the application note Cell Sorting Directly to the C1 IFC and the associated C1 cell sorting workbook today.

For Research Use Only. Not for use in diagnostic procedures.

The promising field of immuno-oncology presents many unanswered questions for scientists in biopharma, cancer research, flow and mass cytometry core facilities and immunology and immuno-oncology academic institutions: How do cancer cells evade the immune system? Which cells and pathways are the best molecular targets? What is the mechanism of action for potential pharmaceuticals? How can we increase tumor immunogenicity? Which biomarkers could predict response? Which drugs offer the best treatment outcomes, and in what order of use?

Approaches based on immunotherapy are providing unprecedented benefits for cancer patients—most importantly, durable responses and complete remission at rates that far surpass conventional chemotherapy. The defining feature of immunotherapy is that T cells and other cell types in the immune system mediate the anticancer response. But immune system cells also promote adverse reactions in some immunotherapy patients. Monitoring T cells and other immune cells in these patients is important for drug development, understanding mechanisms of action and determining biomarkers that correlate with both response and adverse events.

“Enabling the immune system to recognize and eliminate tumors has tremendous potential to change the way cancer is treated and eventually cured. Using the unique power of mass cytometry, the immuno-oncology research community can identify new biomarkers and optimize the development of new cancer immunotherapies to fully realize the potential of this transformative approach to cancer care.”
—Chris Linthwaite, President and CEO, Fluidigm

The Maxpar® Human T Cell Immuno-Oncology EX Panel Kit—together with the Human T Cell Phenotyping Panel Kits—enables comprehensive identification of all major T cell subsets for determining activation, homing status and checkpoint molecule expression. Designed for use with mass cytometry, with capabilities for measuring more than 40 parameters per cell with little or no signal overlap, these panels reveal highly valuable information from even the most limited biological samples.

Modular configuration makes it easy to combine T Cell Phenotyping Panel Kits for flexible or complete coverage. Individual antibodies offer further customization for specific research needs. With access to a growing catalog of more than 600 commercially available preconjugated antibodies and custom conjugation options, the Maxpar panel system can be adapted to meet changing needs in cancer immunotherapy research.

A new industry standard

“The dynamic nature and inherent complexity of the antitumor immune response requires new approaches to deeply profile cell populations at single-cell resolution,” said Fluidigm President and CEO Chris Linthwaite. “This new set of multiparameter panels will empower more researchers with high-dimensional tools to interrogate the tumor immune response and the tumor microenvironment, maximizing the information obtained from each precious sample.”

“Enabling the immune system to recognize and eliminate tumors has tremendous potential to change the way cancer is treated and eventually cured,” Linthwaite added. “Using the unique power of mass cytometry, the immuno-oncology research community can identify new biomarkers and optimize the development of new cancer immunotherapies to fully realize the potential of this transformative approach to cancer care.”

Mass cytometry is fast becoming an industry standard for deep cellular profiling in translational and clinical research. Referenced by hundreds of peer reviewed publications, mass cytometry expands beyond the inherent technical limitations of flow cytometry. With minimal spectral overlap, the technology enables researchers to interrogate more than 40 parameters simultaneously from millions of cells across both intracellular and extracellular protein markers.

Sample case study

As an example, The Journal of Immunology published a paper by Rituparna Das et al., “Combination therapy with anti-CTLA-4 and anti-PD-1 leads to distinct immunologic changes in vivo,” demonstrating highly multiplexed phenotyping of circulating immune cells to characterize immune response to individual and combination therapies. The report detailed the team’s experimental approach in a 45-patient cancer study at Yale University and Memorial Sloan Kettering Cancer Center.

Das and her collaborators used mass cytometry to perform multiparameter immunophenotyping of human PBMCs from patients before and after they were administered anti-PD-1 and/or anti-CTLA-4 checkpoint blockade therapy. Their customized 20-marker panel included the 16-marker Maxpar Human T Cell Phenotyping Panel Kit. They reported that the population of Ki-67+ cells increasing after anti-CTLA-4 or combination checkpoint blockade had a phenotype of CD45RO+, CCR7−, CD27+, CD28+ and CD95+, “consistent with transitional memory T cells.” These same proliferating cells also upregulated MHC class II HLA-DR.

Such deep profiling and identification of changes in this unique cell population would have been difficult using traditional approaches. Our new T cell immuno-oncology panel sets offer even deeper profiling than those used in the study cited above. Combining Maxpar T cell and immuno-oncology panels creates an unprecedented tool for profiling T cells. These panel sets also illustrate the power of mass cytometry as the premier platform for immune profiling and monitoring applications in translational and clinical research.

Register for the 6th Annual Mass Cytometry Summit in Boston on June 9 to learn about recent insights made using mass cytometry and the Maxpar Human T Cell Immuno-Oncology EX Panel Kit.

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For Research Use Only. Not for use in diagnostic procedures.

As single-cell research expands around the globe, researchers are profiling greater numbers of cells to identify new cellular subtypes. Scientists can then explore the role and function of each cell population in health and disease states by characterizing their genotypic, transcriptional, epigenetic and proteomic phenotypes. The C1™ system supports more automated single-cell applications than any other platform, enabling greater understanding of cellular diversity and function across many areas of disease research.

The new C1 Single-Cell mRNA Seq HT IFC is designed to expand current understanding of cellular heterogeneity by empowering scientists studying cancer, stem cells and organismal development with better research capabilities, improved single-cell capture and high-efficiency workflow performance. Isolate up to 800 medium size (10–17 µm) single cells for mRNA sequencing analysis.

“The release of the new medium-cell HT IFC with higher single-cell capture performance is exciting. With this new offering on the C1 system, researchers have a powerful new tool to explore the diversity of cell populations at single-cell resolution, discover rare and novel cell types and characterize their role in life.”
—Chris Linthwaite, Fluidigm President and CEO

Improved reagents, better gene detection

Together with the C1 Single-Cell mRNA Seq HT Reagent Kit v2, the medium HT IFC (high throughput integrated fluidic circuit) detects thousands of genes per cell using 3′ end counting and delivers excellent sensitivity, with design elements that provide powerful control over experimental costs and data quality. New HT product pricing makes this advanced technology more accessible while enabling larger single-cell studies.

“The release of the new medium-cell HT IFC with higher single-cell capture performance is exciting,” said Fluidigm President and CEO Chris Linthwaite. “With this new offering on the C1 system, researchers have a powerful new tool to explore the diversity of cell populations at single-cell resolution, discover rare and novel cell types and characterize their role in life.”

Clear insights

The new medium-cell HT IFC empowers researchers to discover and characterize critical cell populations that remain virtually invisible in the absence of single-cell resolution. It’s a development that promises to reveal fresh scientific insights into the biological roles of rare cell types.

Learn more about the C1 system and the power of microfluidics with single-cell IFCs.

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For Research Use Only. Not for use in diagnostic procedures.

The proven Biomark™ HD automated PCR system continues to empower research advances around the globe. Using the Biomark system’s range of genomic applications, laboratories are reaching new levels of cost efficiency and scalability. Learn why so many scientists rely on this powerful PCR platform and the research it enables.

Growing reference library

You can directly access the growing list of peer publications using the Biomark HD system page in the Support section at fluidigm.com. Search, select and save any of the hundreds of Biomark papers by application, year or journal. You can also find publication titles by disease areas like immuno-oncology or select from a list of topics relevant across all product lines.

Immunotherapy publication spotlight

A 2016 immuno-oncology study published in The Lancet describes the experimental approach of a multicenter cancer clinical trial conducted on the PD-L1 antibody (atezolizumab). In the paper, Atezolizumab versus docetaxel for patients with previously treated non-small-cell lung cancer, Louis Fehrenbacher et al. discuss selecting 12 genes related to immune cell biology and performing Biomark gene expression analysis with the 96.96 IFC and TaqMan® assays on FFPE tumor samples. The team found that atezolizumab improved overall survival in patients with tumors characterized by high gene expression of a T effector and interferon γ gene signature. This important publication concluded that Biomark gene expression analysis contributes to understanding cancer immunotherapy and provides a starting point for developing future predictive biomarkers.

The Biomark HD platform

A flexible system for mid-to-high-throughput gene expression, genotyping, CNV analysis, end-point PCR and digital PCR, Biomark HD delivers significant cost efficiencies over traditional plate-based qPCR methods. Biomark HD reduces the cost per sample by miniaturizing sample and reagent consumption to nanoliter volumes while minimizing hands-on time.

Combine proven, automated workflows with a complete line of IFCs supporting a range of sample and assay numbers to scale to higher sample throughput easily—without changing instruments or technologies.

• Flexible: Access multiple high-performance genomic applications, all on a single system. Easily configure automated workflows with commercial assays and reagents like TaqMan and Delta Gene™ with flexible panel design. Add or remove PCR assays over time, so your assay panel will always be up to date with minimal overhead.
• Efficient: The Biomark system’s significant operational cost efficiencies make it a must-have for mid-to-high-throughput projects. Nanoliter reaction volumes translate to lower master mix, reagent and consumable outlays. And it’s less labor-intensive, thanks to automated operation capabilities that you can set to run unattended.
• Scalable: With Biomark, you can seamlessly scale your project design using the same technology—from small pilot studies of up to 12 samples per run to larger experiments with as many as 192 samples per run. With greater efficiencies and higher throughput than traditional methods, you can efficiently manage throughput demands and achieve results, within project timelines.
• Trusted: Achieve high-quality results with performance comparable to established qPCR platforms that serve critical gene expression and genotyping applications in cancer, immunotherapy and other areas of translational and clinical research.

Contact us to learn how you can easily transition your qPCR assays to the Biomark HD system to achieve new economies of scale.

For Research Use Only. Not for use in diagnostic procedures.

Next-generation sequencing (NGS) has been instrumental in advancing the understanding of human health and disease. Growing demand for sequencing around the world is driving the need for workflow improvements and cost efficiencies.

Enter Juno™, the industry’s only fully programmed benchtop nanofluidics system, built to scale genomics workflows to optimum efficiency. The platform’s newest commercial application is targeted DNA sequencing library prep, which includes everything needed to prepare NGS-ready libraries including integrated custom assay design services.

High capacity

Juno library prep is optimized for use with Illumina® sequencing systems, bringing new sequencing efficiencies to labs running targeted NGS assays on the mid- to high-throughput scale. With processing capacity of up to 192 samples per run, sample throughput is at least twice that of other systems available today. One operator with a single Juno instrument can prepare up to 1,536 NGS-ready targeted DNA libraries weekly. For labs processing smaller batch sizes, Juno provides the same benefits of expedient turnaround time and walkaway workflow, yielding highly consistent NGS-ready amplicon libraries.

Flexibility

Juno library prep chemistry enables a range of assay panel options. You can amplify up to 4,800 amplicons per sample, access expert design services and ready-to-use primer delivery. Plus, the ability to add amplicon assays over time ensures your panel content stays up to date. Additionally, Juno targeted DNA library prep for NGS can operate overnight without monitoring, maximizing productivity over 24 hours.

“We are pleased to announce the Juno Targeted DNA Sequencing Library Preparation System as an expansion of our growing portfolio of automated genomic workflows that increase laboratory efficiency for medium-to-high-throughput pipelines,” said Steve McPhail, General Manager of Clinical and Applied Markets at Fluidigm. “We are now able to offer our customers a significant improvement over the largely manual, low-throughput and laborious NGS library preparation workflows used today.”

Learn more about new Juno Targeted DNA Sequencing Reagents.

Since we launched the redesigned Fluidigm website in 2014, we’ve had our sights on delivering an insightful online customer experience, and we’ve been delivering on that pledge. It’s our priority to provide excellent service for your state-of-the-art single-cell analysis and production genomics research systems and tools. You have the freedom to access the full fluidigm.com digital catalog anytime. Search contextually by platform, application or keyword to easily find IFCs and reagents, antibodies for mass cytometry experiments, and parts and services.

Growing content library

Increased product visibility simplifies your quest for informative content about your research in growing applications like cancer immunotherapy, oncology, immunology and other health and disease studies. Discover the depth of online resources at fluidigm.com, including feature articles, scientist spotlights, webinars, videos, publication downloads and news—and we’re constantly adding more. Already know what you want? Use the smart-search function to quickly run queries for interviews with specialized experts and product information.
Fluidigm

“We continue to expand the support and services available to our scientist customers, and providing informative content and online catalog access are two of the latest improvements. Partnering with customers is an ideal opportunity to do our part to advance the understanding of biological processes.” 
— Paul Steinberg, Sr. VP, Commercial Operations

Fluidigm

Digital catalog

Use the digital catalog to quickly perform filtered searches and refine results through the menu or drill down further by keyword to narrow your results. Frequently searched items highlighted at the top of the page minimize searching. Product detail pages open in a tab to reveal kit contents, chemistries, sizes and links to supporting technical and safety documentation. Kits are clearly itemized for a detailed understanding of components and differences. View and compare to ensure proper item selection for bulk genomics and single-cell investigations.

For example, the all-new Reagents section features product pages with chemistry overviews and information about sampling processes. Search by item name or product number for filtered results and purchasing options. There are already a dozen reagent family product pages with rich application detail. We’ll continue adding new ones, so check back for more.

New ordering options

North American customers can place orders online and view their purchasing history to see past transaction details and easily modify and replicate orders. Customers in the US and Canada who have a Fluidigm account are already registered for online ordering. New customers will find it easy to set up an online account to place orders, view past order history and see current order confirmations. Online web ordering offers numerous options for finding and purchasing consumables and parts for your Fluidigm systems. 

The view ahead

“Life science researchers around the world are using Fluidigm instruments to transform what we know about health and disease,” said Paul Steinberg, senior vice president of commercial operations. “We continue to expand the support and services available to our scientist customers, and providing informative content and online catalog access are two of the latest improvements. Partnering with customers is an ideal opportunity to do our part to advance the understanding of biological processes.”

Our mission at Fluidigm is to simplify the complexity of understanding and applying biology. We hope you find this resource a valuable addition to our website. If you have thoughts to share, we welcome your feedback.

To receive updates about Fluidigm news, products, events and webinars, sign up for our email newsletter.

As part of our ongoing commitment to support our customers and aid in their success, we’ve opened a Fluidigm customer inspiration center in Markham, Ontario, the area of Greater Toronto that is Canada’s tech capital and the birthplace of mass cytometry. We developed this functional facility to provide customers with a firsthand view of CyTOF^® technology on Helios™, the most advanced mass cytometry system ever built.

“Our new mass cytometry customer inspiration center was developed in response to increasing interest from our customers,” said Dmitry Bandura, Vice President of Research and Development at Fluidigm. “While our new center will initially enable demonstrations of mass cytometry, we plan to expand this center in the future to include training courses to certify new users on best practices using this transformational technology.”

Mass cytometry continues to make news. Hundreds of peer-reviewed publications cite mass cytometry’s instrumental role in revealing novel insights in health and disease. Uniquely enabling high-parameter analysis of millions of cells at single-cell resolution, Helios empowers researchers to transcend the limitations of flow cytometry. Investigators can efficiently design and implement highly multiplexed antibody panels across numerous cell surface and intracellular protein markers.

With more than 600 preconjugated antibody options and the flexibility to conjugate new antibodies for tailored experiments, mass cytometry is fast becoming a standard method for deeply profiling precious translational and clinical research samples across cancer, immunology, cancer immunotherapy and other critical areas of research.

The opening of the new customer inspiration center reflects our passion to fuel new discoveries and insights at single-cell resolution. Together with you, we look forward to extending the power of mass cytometry around the world in our ongoing mission to advance understanding of human health and complex diseases.

To receive updates about mass cytometry and the customer inspiration center and be notified about upcoming events and webinars, sign up for our email newsletter. Visit fluidigm.com for more Helios services, or contact your local Support team.

Time-of-flight mass cytometry, the technology behind CyTOF^® instruments, has shot to prominence as a game-changing innovation powering unprecedented breakthroughs in health and disease. With capability to perform high-parameter analysis of millions of cells at single-cell resolution, mass cytometry is a crucial tool for studying cellular processes in cancer, immunology and cancer immunotherapy.

On June 10, Fluidigm sponsored the 5th Annual Mass Cytometry Summit to gather the scientific community for a colloquy on moving the field ahead. More than a hundred scientists from 12 nations convened at the Seattle event for presentations from leading researchers revealing emerging insights made through mass cytometry. A few highlights included Hartland Jackson’s presentation on the visual impact of imaging using mass cytometry, Erin Simonds’ illuminating discussion of high-dimensional data analysis tools and a lively panel discussion on approaches to interrogate tumors and tissues.

“Amazing. I haven’t been so excited to be part of a conference in a long time. Hearing the presentations on analysis of mass cytometry data was huge for me, really helpful.”
—Evan Lind, PhD

“This combination of information collected on single cells is what we need to characterize dynamic, evolving cellular systems like cancer and immune cells from patients being treated with combinations of targeted therapy and immunotherapy,” noted speaker Jonathan Irish, PhD.

“Today we are discovering cell subsets that predict patient treatment responses based on cell-signaling responses,” he continued. “Tomorrow I hope to be able to mine someone’s published single-cell RNA-seq data to see what transcripts are expressed in these cells, … see with imaging data where those cells exist in the tumor … or know how they will respond to a drug from a high-throughput screen.”

Here’s a recap of the speakers and topics from this year's three-part event:

Mass Cytometry and Human Health

• Massively Multiplexed Analysis in Developing Human Systems: Sean Bendall, PhD, Stanford University
• IL-2 Induces Selective Activation of Helios-Positive Regulatory T Cells and CD56bright NK Cells in Vitro and in Patients with Chronic GVHD Receiving Low-Dose IL-2 Therapy: Nicole Paul, MS, Dana-Farber Cancer Institute
• Human Systems Immunology Enabled by Mass Cytometry: Petter Brodin, MD, PhD, Karolinska Institutet, Sweden
• Standardization and Reproducibility in Mass Cytometry Assays: Mike Leipold, PhD, Stanford University

Extracting Meaning from Complex Data

• Tools and Approaches for Analysis of Mass Cytometry Data: Erin Simonds, PhD, UCSF
• Fresh Squeezed: Using Citrus and Other New Improvements in Cytobank: Geoff Kraker, Cytobank

Meeting the Challenge of Tissue and Tumor Analysis

• Highly Multiplexed Imaging of Tumor Tissues by Mass Cytometry for Precision Medical Applications: Hartland Jackson, PhD, University of Zurich, Switzerland
• Using Mass Cytometry to Interrogate Tumors and Tissues: Panel discussion moderated by Sean Bendall, with Jonathan Irish, PhD, Vanderbilt; Adeeb Rahman, PhD, Mount Sinai Hospital; and Hartland Jackson

“Amazing,” said cancer immunologist and Assistant Professor Evan Lind, PhD. “I haven’t been so excited to be part of a conference in a long time. Hearing the presentations on analysis of mass cytometry data was huge for me, really helpful.”

“I was inspired hearing from the scientists about all the diverse projects being done with mass cytometry,” Lind added. “It gave me a lot to think about.”

There is still much to learn about how the immune system recognizes and eliminates tumors that will change the course of cancer treatment in the future. Interrogation of immune cell function and the tumor microenvironment at single-cell resolution is essential, and the summit highlighted a number of advantages that CyTOF technology provides to achieve this goal.

Imagine what discoveries and scientific advancements lay in store for the next Mass Cytometry Summit in 2017. We look forward to seeing you there.

To receive updates about mass cytometry and be notified about upcoming events and webinars, sign up for our email newsletter.

When we introduced Script Hub™ as an open-source platform for C1™ methods and applications, we invited the single-cell community to join us on a quest. The mission: Develop an array of innovative single-cell applications to uncover biological diversity and discover the functional role of unique cell populations in health and disease.

Scientists from around the world have responded and are sharing their groundbreaking protocols and data with the entire C1 user community. This information is available for everyone to access on Script Hub, and features novel single-cell applications for epigenetics, T cell receptor sequencing, DNA sequencing and more.

Here’s an overview of one of the most-visited areas on Script Hub, where C1 mRNA sequencing methods including full-length mRNA seq and transcript counting deliver unparalleled breadth and value for your single-cell analysis.

Full-length mRNA sequencing

Sequencing of full-length transcripts is crucial for uncovering deep insights into the biology of individual cells. The approach offers single-base resolution of the RNA sequence to yield a highly detailed view of each transcript. Measure individual gene expression and quantify allele or splice-variant expression, map transcriptional start sites, identify alternative splicing patterns and discover novel transcripts or gene fusions.

Several specialized approaches are now available on Script Hub to power your single-cell studies, including:

• C1 TCR Seq: T cell receptor sequencing leverages the detail of whole transcriptome analysis to simultaneously reconstruct the variable region of the TCR and identify all other genes that regulate each T cell’s function. TCR seq brings together full-length mRNA sequencing with TraCeR, a powerful new bioinformatics tool. For a deeper dive into single-cell TCR seq, read our interview with TraCeR’s developers.
• C1 SMART Seq^®: Amplifying full-length cDNA for mRNA sequencing empowers C1 discovery experiments. SMARTer^® and C1 SMART Seq2 allow you to create reverse-transcribed poly(A) RNA and employ specialized template-switch technology to generate full-length cDNA prior to next-generation sequencing.

For a complete list of protocols available for full-length sequencing on the C1 system, see Table 1.

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Full-Length Methods

Script Name	Reverse Transcription Method	Amplification Method	Analysis Method	Developer	Advantages
C1 SMARTer v1	Poly(A), template switch	PCR	Full-length	Fluidigm	Standard protocol on all C1 systems
C1 SMART Seq2	Poly(A), template switch	PCR	Full-length	Oxford	Generate longer cDNA
Full-length mRNA Sequencing (SMART Seq v4)	Poly(A), template switch	PCR	Full-length	Clontech	New RT and DNA polymerase with greater sensitivity than SMARTer v1
TCR Sequence Determination by TraCeR	Poly(A), template switch	PCR	Full-length	Wellcome Trust Sanger Institute	Provides a more comprehensive view of the T cell repertoire

Table 1. Full-length sequencing protocols available on Script Hub
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Transcript counting methods

Determine relative numbers of transcripts expressed by each cell with quantitative transcript counting for single-cell gene expression. It’s a cost-effective way to rapidly survey cellular heterogeneity and identify novel cell populations. There are two common approaches to transcript counting by RNA sequencing:

• 3′ end counting: This frequently-used method leverages molecular tags on the polyadenylated region of the gene to detect transcripts differing in either the sequence of 3′ terminal exon or the length of the 3′ untranslated region (UTR) of the transcript. It offers the benefit of separating coding RNA from non-coding RNA during reverse transcription.
• 5′ end counting: This approach uses tags against the 5′ end of the transcript to identify transcription start sites and promoters. Leveraging the resulting information aids in identifying promoter usage or transcription factor binding sites.

For a complete list of C1 protocols available on Script Hub for transcript counting methods, see Table 2.
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Transcript Counting Methods

Script Name	Reverse Transcription Method	Amplification Method	Analysis Method	Developer	Advantages
C1 mRNA Seq HT	Poly(A), template switch	PCR	3'	Fluidigm	On-IFC cell barcoding simplifies sample handling and reduces library prep and sequencing costs.
C1 STRT Seq	Poly(A), template switch	PCR	5'	Karolinska Institute	Detects long non-coding RNAs and non-poly(A) transcripts
C1 CEL Seq	Poly(A)	in vitro transcription	3'	Technion – Israel Institute of Technology	PCR-based amplification alternative
C1 CAGE	Random priming, template switch	PCR	5'	RIKEN Institute	Detects capped RNA transcripts; users can share data with the FANTOM5 consortium.

Table 2. Transcript counting protocols available on Script Hub
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Maximize the power of your single-cell analysis on the C1 system, with access to the largest collection of single-cell genomics applications in the industry. Use these innovative mRNA sequencing protocols on Script Hub together with Open App™ IFCs to advance your single-cell studies. Join us on the quest to simplify the complex and reveal new insights into the biology of life.