Comparison of Evercode™ WT v3 and Chromium™ GEM-X Single Cell 3’ Kit v4 in Mouse Brain Nuclei

November 13, 2025/in Parse/by Harshita Sharma

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Comparison of Evercode™ WT v3 and Chromium™ GEM-X Single Cell 3’ Kit v4 in Mouse Brain Nuclei

Comparison Highlights

Evercode WT v3 delivers superior gene detection in head-to-head sensitivity tests.
Cell type proportions remain consistently represented.
Analysis of differential gene expression shows Evercode WT v3 identifies 2× more genes than competing methods.

Study Overview
Two embryonic mouse brains were sagittally dissected and flash-frozen by a third-party vendor.
One half from each brain was processed by a 10x Genomics certified provider for nuclei isolation and library preparation, while the other halves were processed by Parse Biosciences using their own workflow.
Sequencing was performed by a third-party, and data analysis was completed using each manufacturer’s respective pipeline.

As the official distributor in Australia and New Zealand, Decode Science makes accessing genomics solutions straightforward. Our role is to connect your lab with advanced technologies, ensuring you get the right solution for your sequencing projects—delivered locally with support when you need it.

Data Set: Parse 10 Million Human PBMCs in a Single Experiment

October 30, 2025/in Parse/by Harshita Sharma

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Scale Single-Cell Research Like Never Before

Key Takeaways

Analyze 10 million cells across 1,152 samples in a single experiment
Increase statistical power by profiling more cells per sample
Capture detailed cellular responses to perturbations and drug treatments

Figure 1: Experimental Design Overview
Approximately 10 million PBMCs from 12 healthy donors were treated with 90 different cytokines in a single GigaLab experiment, covering 1,092 experimental conditions.

Cells were thawed, washed, and seeded at 1 million cells per well across 12 plates. After 24-hour cytokine treatment, cells were fixed, barcoded, and processed for whole transcriptome sequencing. Libraries were sequenced on the Ultima Genomics platform, achieving ~31,000 reads per cell, with 62.45% cell retention after barcoding.

Results?

After data processing with the Parse Analysis Pipeline v1.4.0, integration, and classification, 9,697,974 cells across 18 immune cell types were identified—including rare populations that are typically missed in smaller experiments. Each condition yielded a median of 7,400 cells, enabling high-resolution analysis of immune responses.

Differential expression analysis identified how cytokines influenced gene activity across cell types. Many cytokines triggered strong transcriptional responses, with over 50 genes upregulated per treatment.

Figure 2: Single-Cell UMAP Overview
9,697,974 PBMCs from 12 donors were integrated with Harmony, clustered using Scanpy, and manually annotated, revealing 18 immune cell types present across all donors and experimental conditions.

Figure 3: Cytokine-Induced Gene Changes
A heatmap summarizes the averaged number of genes significantly upregulated (log fold change >0.3, p <0.001) for each cell type and cytokine, highlighting which immune cells respond most strongly to specific cytokine treatments.

Example tutorial vignettes from Parse Biosciences and Fabian Theis’ lab at Helmoltz-Munich:

Parse 10M PBMC Cytokines Clustering Tutorial
Joey Pangallo, Efi Papalexi – Parse Biosciences, Seattle, WA
Step-by-step example of analyzing 10 million PBMCs treated with cytokines using the Evercode workflow. Covers data loading, preprocessing, Leiden clustering, and generating UMAP plots with Scanpy.

Parse 10M PBMC Cytokines Clustering Tutorial (Downsampled)
Joey Pangallo, Efi Papalexi – Parse Biosciences, Seattle, WA
Same workflow as above, starting with a downsampled dataset of 1 million cells. Ideal for quicker exploration or limited CPU memory setups.

scCODA Parse 10M PBMC Cytokines
Artur Szałata, Dominik Klein, Soeren Becker, Fabian Theis – Helmholtz-Munich
Demonstrates analysis of cell proportion changes across 10 million PBMCs. Shows how using the full dataset improves statistical significance of perturbation effects. Based on scCODA, a Bayesian model for compositional single-cell data analysis (Nat Commun 12, 6876, 2021).

Parse 10M PBMC Cytokines Dask Workflow
Artur Szałata, Dominik Klein, Soeren Becker, Fabian Theis – Helmholtz-Munich
Walks through preprocessing the 10M cell dataset using Dask. Loads data chunk-wise to reduce memory use and demonstrates highly variable gene selection for downstream analysis.

Dataset License: CC BY-NC 4.0 (non-commercial use). Commercial licensing inquiries: support@parsebiosciences.com

QUICK DOWNLOAD FILES

10M PBMC 12donor 90cytokines h5ad (212 GB)

Parse 10M PBMC cytokines clustering tutorial

Parse 10M PBMC cytokines clustering tutorial on downsampled data

scCODA Parse 10M PBMC cytokines

Parse 10M PBMC cytokines Dask workflow

As the official distributor in Australia and New Zealand, Decode Science makes accessing genomics solutions straightforward. Our role is to connect your lab with advanced technologies, ensuring you get the right solution for your sequencing projects—delivered locally with support when you need it.

Evercode TCR Mega

February 21, 2024/in Evercode, Parse, Partners/by Harshita Sharma

PRODUCTS

Evercode TCR Mega

Unlock scalable immune profiling capabilities with Evercode™ TCR Mega, empowering you to analyze up to 1 million cells at a time. In the intricate landscape of immunity, comprehensive data is key. With Evercode™ TCR Mega, you can achieve unparalleled resolution in studying TCR clonotype diversity and T-cell states.

Benefit from the expansive scale of Evercode™ TCR Mega, which offers a host of advantages alongside the wealth of information provided by WT profiles. Whether you’re exploring immune responses, investigating cellular dynamics, or delving into immunotherapy research, Evercode™ TCR Mega equips you with the tools to navigate the complexities of the immune system with confidence and precision.

Up to 1 million cells in a single experiment

Experience the power of scale with Evercode. Conduct experiments with up to 1 million cells in a single run, unlocking the immense diversity within the immune repertoire like never before. With Evercode, identify an extensive array of TCR clonotypes, providing unparalleled insights into immune function and response.

Not only can Evercode detect clonotypes, but it also offers the capability to map them to T cell subtype clusters. By analyzing gene expression profiles from nearly 1 million T cells isolated from PBMCs, Evercode enables the classification of cells into distinct T cell subtypes. This comprehensive approach ensures a deeper understanding of immune dynamics and facilitates more nuanced analysis of immune responses.

High TCR detection in activated and primary T cells

Experience outstanding TCR detection in both activated and primary T cells with our cutting-edge profiling techniques. In our investigation, T cells derived from peripheral blood mononuclear cells (PBMCs) underwent two distinct conditions: direct profiling (Primary) and activation through culture for 3 days with CD3/CD28 beads and IL-2 (Activated).

Our results demonstrate robust TCR detection in both experimental conditions, highlighting the versatility and reliability of our methodology across diverse T cell states. Whether profiling primary T cells or their activated counterparts, our approach ensures accurate and comprehensive characterization of the TCR repertoire, providing invaluable insights into immune responses and cellular dynamics.

Trust in our advanced profiling techniques to deliver precise and high-fidelity data, enabling a deeper understanding of T cell biology and immunological processes. With our innovative methodologies, delve into the complexities of the immune system with confidence and clarity, paving the way for transformative discoveries in immunology.

Comprehensive immune repertoire detection

Immerse yourself in unparalleled detection of the immune repertoire with the Evercode™ TCR kit, meticulously crafted to offer the most comprehensive profile attainable. In a groundbreaking study spanning 8 donors, our kit revealed the identification of nearly 500,000 unique beta chain clonotypes.

Notably, the majority of these clonotypes were deemed rare, emphasizing the remarkable sensitivity and depth of our detection capabilities. With the Evercode™ TCR kit at your disposal, you gain the ability to unveil the complete spectrum of immune diversity, from commonplace to exceptionally rare clonotypes. This empowers you to delve into the intricacies of immune responses with unparalleled precision and breadth, opening new avenues for exploration and discovery in immunology.

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Evercode TCR

February 21, 2024/in Evercode, Parse, Partners/by Harshita Sharma

PRODUCTS

Evercode TCR

Explore the depths of the immune repertoire with our cutting-edge solution: single-cell TCR profiling combined with whole transcriptome analysis—no additional instrumentation required.

With our state-of-the-art technology, you can detect TCRs with remarkable sensitivity while simultaneously capturing transcriptome-wide gene expression, including essential T-cell subtype markers. Delve into the intricate cellular landscape and unlock unprecedented insights by examining paired alpha and beta sequences within individual cells.

This revolutionary approach empowers you to unravel the complex interplay between TCR diversity and gene expression profiles at the single-cell level, providing a holistic understanding of immune responses and cellular heterogeneity. Bid farewell to the constraints of conventional methods and embark on a transformative journey in immunogenomics research with our integrated solution.

High TCR detection in activated and primary T cells

Witness exceptional TCR detection in both activated and primary T cells through our state-of-the-art profiling techniques. In our investigation, T cells sourced from peripheral blood mononuclear cells (PBMCs) underwent two distinct conditions: direct profiling (Primary) and activation via culture for 3 days with CD3/CD28 beads and IL-2 (Activated).

Our findings reveal robust TCR detection in both experimental conditions, underscoring the versatility and dependability of our methodology across various T cell states. Whether profiling primary T cells or their activated counterparts, our approach guarantees precise and comprehensive characterization of the TCR repertoire, offering invaluable insights into immune responses and cellular dynamics.

Rely on our advanced profiling techniques to deliver meticulous and high-fidelity data, facilitating a deeper comprehension of T cell biology and immunological processes. With our innovative methodologies, explore the intricacies of the immune system with confidence and clarity.

Comprehensive immune repertoire detection

Experience unparalleled detection of the immune repertoire with the Evercode™ TCR kit, designed to provide the most comprehensive profile available. In a groundbreaking study encompassing 8 donors, our kit identified nearly 500,000 unique beta chain clonotypes.

Remarkably, the vast majority of these clonotypes were classified as rare, highlighting the sensitivity and depth of our detection capabilities. With the Evercode™ TCR kit, you can uncover the full spectrum of immune diversity, from common to exceedingly rare clonotypes, empowering you to explore the intricacies of immune responses with unprecedented precision and breadth.

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Let’s Find You an Application That Helps Your Research

Get a call from your local Decode Science representative to help you find the best fit genomics products for you.

Or give us a call at:

1300 581 991

Evercode TCR Mini

February 21, 2024/in Evercode, Parse, Partners/by Harshita Sharma

PRODUCTS

Evercode TCR Mini

Unlock the complexity of the immune repertoire with our innovative solution: single-cell TCR profiling combined with whole transcriptome analysis—all without the need for additional instrumentation.

With our advanced technology, you can achieve sensitive detection of TCRs while simultaneously measuring transcriptome-wide gene expression, including crucial T-cell subtype markers. Dive deep into the cellular landscape and gain unparalleled insights by analyzing paired alpha and beta sequences within the same cell.

This groundbreaking approach empowers you to uncover the intricate interplay between TCR diversity and gene expression profiles at the single-cell level, providing a comprehensive understanding of immune responses and cellular heterogeneity. Say goodbye to the limitations of traditional methods and embark on a new era of immunogenomics research with our integrated solution.

High TCR detection in activated and primary T cells

Experience high TCR detection in both activated and primary T cells with our advanced profiling techniques. In our study, T cells isolated from peripheral blood mononuclear cells (PBMCs) underwent two distinct conditions: direct profiling (Primary) and activation through culture for 3 days with CD3/CD28 beads and IL-2 (Activated).

Our results demonstrate robust TCR detection in both scenarios, showcasing the versatility and reliability of our methodology across different T cell states. Whether profiling primary T cells or activated counterparts, our approach ensures accurate and comprehensive characterization of the TCR repertoire, providing invaluable insights into immune responses and cellular dynamics.

Count on our advanced profiling techniques to deliver precise and high-quality data, enabling deeper understanding of T cell biology and immunological processes.

Ready to Order?

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Let’s Find You an Application That Helps Your Research

Get a call from your local Decode Science representative to help you find the best fit genomics products for you.

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1300 581 991

Evercode WT Mega

February 21, 2024/in Evercode, Parse, Partners/by Harshita Sharma

PRODUCTS

Evercode WT Mega

Streamline the scaling of your single-cell projects with Evercode™ split-pool combinatorial barcoding. This innovative technique offers a straightforward, instrument-free solution to single-cell sequencing, revolutionizing the process with its simplicity and versatility.

With Evercode™, you can effortlessly adopt a highly sensitive approach to single-cell sequencing, regardless of your lab’s resources or expertise level. The simplicity of this method makes it accessible to researchers of all backgrounds, while still delivering unparalleled sensitivity, scalability, and flexibility.

Say goodbye to complex instrumentation and cumbersome protocols. Evercode™ empowers labs of any size to embark on single-cell sequencing projects with confidence, paving the way for groundbreaking discoveries in cellular biology and beyond.

Experience a revolution in gene detection sensitivity with Evercode WT v2.

In a rigorous comparative study conducted on mouse brain samples, Evercode WT v2 demonstrated exceptional superiority over the Chromium Next GEM Single Cell 3’ Kit v3.1. Impressively, Evercode WT v2 detected an average of 84% more genes at a common read depth target of 20,000 reads per cell.

With Evercode WT v2 at your disposal, you gain the power to uncover a broader spectrum of genes and dive deeper into gene expression profiles. This invaluable wealth of information will enrich your research endeavors, providing nuanced insights into cellular dynamics and molecular processes. Elevate your single-cell transcriptomics studies to unprecedented heights with the unmatched sensitivity and precision offered by Evercode WT v2.

Evercode™ delivers more results per experiment

Evercode™ sets a new standard by delivering more results per experiment compared to leading droplet-based technologies. This means that with Evercode™, you can achieve your research goals with significantly fewer experiments, saving time, resources, and effort.

By maximizing the efficiency of each experiment, Evercode™ allows you to generate more data and insights in less time. Whether you’re exploring gene expression profiles, investigating cellular heterogeneity, or uncovering novel biological pathways, Evercode™ streamlines the process and accelerates your research progress.

With Evercode™, you can optimize your experimental workflow and achieve more impactful results with fewer resources expended. Experience the difference that Evercode™ can make in advancing your scientific discoveries and pushing the boundaries of single-cell analysis.

Fix now, run later

Our innovative technology allows you to fix cells or nuclei as soon as they’re available, effectively preserving the biological integrity until you’re ready to proceed with your experiments. With just a 30-minute fixation process, your samples remain stable for up to 6 months.

This approach offers unparalleled flexibility in your research workflow. Whether you’re conducting a timecourse study, collaborating across multiple laboratories, or need to segregate sample preparation from core lab space, fixation provides the freedom to work according to your schedule and preferences.

With Evercode™, you can confidently lock in the biology of your samples, knowing that they’ll be ready for analysis whenever you are. Say goodbye to time constraints and logistical challenges – embrace the flexibility of fixation with Evercode™.

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Evercode WT

February 21, 2024/in Evercode, Parse, Partners/by Harshita Sharma

PRODUCTS

Evercode WT

Realize your single-cell aspirations with Evercode™ split-pool combinatorial barcoding. This straightforward, instrument-free solution revolutionizes single-cell sequencing, offering unparalleled sensitivity, scalability, and flexibility to labs of any size.

With Evercode™, you can effortlessly adopt a highly sensitive approach to single-cell sequencing, empowering you to unlock the complexities of cellular heterogeneity with ease. Scale your experiments to new heights while maintaining precision and reliability, thanks to Evercode’s adaptable design and seamless workflow.

Say goodbye to cumbersome instrumentation and complex protocols – Evercode™ simplifies single-cell sequencing, making it accessible to researchers at all levels. Whether you’re exploring the intricacies of developmental biology, investigating immune responses, or unraveling the mysteries of cancer heterogeneity, Evercode™ equips you with the tools you need to achieve your single-cell ambitions.

Higher Sensitivity with Evercode WT v2

Embark on a journey of unparalleled sensitivity in gene detection with Evercode WT v2. In a comprehensive comparative study conducted on mouse brain samples, Evercode WT v2 demonstrated remarkable superiority over the Chromium Next GEM Single Cell 3’ Kit v3.1. Remarkably, Evercode WT v2 detected an average of 84% more genes at a common read depth target of 20,000 reads per cell.

With Evercode WT v2 as your tool of choice, you can uncover a broader spectrum of genes and delve deeper into gene expression profiles. This invaluable information will enrich your research endeavors, providing nuanced insights into cellular dynamics and molecular processes. Elevate your single-cell transcriptomics studies to unprecedented heights with the unmatched sensitivity and precision offered by Evercode WT v2.

Boost the signal, reduce the noise

Elevate signal quality and minimize noise in your single-cell RNA sequencing (scRNA-seq) experiments with Evercode™. Multiplets, a common challenge in scRNA-seq approaches, can complicate data analysis and obscure biological insights. By adopting Evercode™, which utilizes a cell-as-reaction-vessel approach, you can eliminate issues associated with multiplets, leading to cleaner and more accurate data.

In a human-mouse species mixing experiment conducted with Evercode™, we achieved an exceptionally low multiplet rate of only 2.3%. This rate significantly outperforms traditional droplet-based approaches, demonstrating Evercode’s™ effectiveness in reducing multiplet interference and enhancing data quality.

With Evercode™, you can confidently boost signal detection while minimizing noise, enabling more precise and insightful analysis of single-cell transcriptomic data. Say goodbye to multiplet-related challenges and unlock the full potential of your scRNA-seq experiments with Evercode™.

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1300 581 991

Evercode WT Mini

February 20, 2024/in Evercode, Parse, Partners/by Harshita Sharma

PRODUCTS

Evercode WT Mini

Introducing Evercode™ WT Mini V2, the revolutionary solution for single-cell whole transcriptome analysis. Designed to operate without the need for additional instruments, the Evercode™ WT Mini V2 allows you to delve into single-cell transcriptomics with ease and convenience.

Key features include:

Compact Design: The Evercode™ WT Mini V2 is perfectly sized for researchers looking to explore single-cell transcriptomics on a smaller scale. Its compact design makes it ideal for generating proof-of-concept results before scaling up to larger platforms.
Quality Results: Experience the exceptional quality of results achievable with Parse technology. The Evercode™ WT Mini V2 enables you to obtain reliable and accurate transcriptomic data from individual cells, providing valuable insights into your biological samples.
Scalability: As your research progresses, seamlessly transition to larger platforms such as the Evercode™ WT or Evercode™ WT Mega to delve deeper into your biology. The Evercode™ WT Mini V2 serves as an ideal starting point for expanding your single-cell transcriptomics studies.

With Evercode™ WT Mini V2, unlock the potential of single-cell transcriptomics and embark on a journey of discovery in your research. Explore the complexities of gene expression at the single-cell level and uncover new insights into cellular heterogeneity and biological processes.

Higher Sensitivity with Evercode WT v2

Experience unmatched sensitivity in gene detection with Evercode WT v2. In a comparative study conducted in mouse brain samples, Evercode WT v2 outperformed the Chromium Next GEM Single Cell 3’ Kit v3.1, detecting an average of 84% more genes at a common read depth target of 20,000 reads per cell.

With Evercode WT v2, you can uncover a broader spectrum of genes and gain deeper insights into gene expression profiles, providing invaluable information for your research endeavors. Elevate your single-cell transcriptomics studies to new heights with the superior sensitivity of Evercode WT v2

Lower multiplet rates than droplet-based approaches

Achieve significantly lower multiplet rates compared to droplet-based approaches with Evercode WT. In a human-mouse species mixing experiment utilizing Evercode WT, we observed an impressively low multiplet rate of only 2.3%. This rate is substantially lower than what is typically encountered with droplet-based methods.

By leveraging Evercode WT, researchers can confidently minimize the occurrence of multiplets, ensuring greater accuracy and reliability in single-cell transcriptomic analysis. This enhanced precision allows for more accurate interpretation of biological data and deeper insights into complex biological systems.

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Dr. Ebru Boslem

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Dr. Ebru Boslem

Evercode TCR Mega

1M CELLS

96 SAMPLES

EXPONENTIALLY SCALABLE

NO INSTRUMENT REQUIRED

UNMATCHED DATA QUALITY

WORKS WITH FIXED CELLS AND NUCLEI

Let’s Find You an Application That Helps Your Research

Evercode TCR

10K CELLS

12 SAMPLES

EXPONENTIALLY SCALABLE

NO INSTRUMENT REQUIRED

UNMATCHED DATA QUALITY

WORKS WITH FIXED CELLS AND NUCLEI

Let’s Find You an Application That Helps Your Research

Evercode TCR Mini

100K CELLS

48 SAMPLES

EXPONENTIALLY SCALABLE

NO INSTRUMENT REQUIRED

UNMATCHED DATA QUALITY

WORKS WITH FIXED CELLS AND NUCLEI

Let’s Find You an Application That Helps Your Research

Evercode WT Mega

1M CELLS

96 SAMPLES

EXPONENTIALLY SCALABLE

NO INSTRUMENT REQUIRED

UNMATCHED DATA QUALITY

WORKS WITH FIXED CELLS AND NUCLEI

Let’s Find You an Application That Helps Your Research

Evercode WT

100K CELLS

48 SAMPLES

EXPONENTIALLY SCALABLE

NO INSTRUMENT REQUIRED

UNMATCHED DATA QUALITY

WORKS WITH FIXED CELLS AND NUCLEI

Let’s Find You an Application That Helps Your Research

Evercode WT Mini

10K CELLS

12 SAMPLES

EXPONENTIALLY SCALABLE

NO INSTRUMENT REQUIRED

UNMATCHED DATA QUALITY

WORKS WITH FIXED CELLS AND NUCLEI

Let’s Find You an Application That Helps Your Research

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