Validation Services

November 24, 2025/in Uncategorized/by Harshita Sharma

NGS Validation Package
– Expert Support for Your Lab

Get your lab NGS-ready with our comprehensive Validation Package, designed for labs with limited experience, staff, or analytical expertise. Our modular approach ensures tailored support for your lab’s needs.

But... Why Akoya Biosciences?

Choose Your Preferred Module

Module 1 - Consultancy Support

Module 2 - Wet Lab Validation Support

Preparation of samples (from extracted DNA), libraries, QC, sequencing
Full report for up to 96 samples
Options for automated or manual preparation
Training session for your team to run samples and generate additional validation data
Estimated Time: From 2 weeks (including documentation & evaluation)

Breaks into phases requiring initial input from your team

Module 3 - Dry Lab Validation Support

Process raw sequencing data or VCF/BAM files
Establish secondary analysis pipeline if needed (in collaboration with Franklin)
Initial high-level analysis to check concordance and troubleshoot issues
Team training session to run cases and generate additional validation data
Estimated Time: From 2 weeks (including documentation & evaluation)

Phased approach requiring starting data from your team

Proud Partnerships

How does it work?

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we’re here to all your questions

How much does it cost

How long it takes?

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What are the deliverables?

MosaiX High-Complexity Library Prep Kit – Early Access Promotion

November 24, 2025/in SeqWell/by Harshita Sharma

MosaiX High-Complexity Library Prep Kit ,
– Early Access Promotion

Be among the first to experience the newest in high-complexity library prep technology.

SeqWell has just launched the MosaiX High-Complexity Library Prep Kit, unveiled at ASHG, and we’re offering a limited-time early-access promotion for researchers in AU & NZ.

5/5

Early-Access Offer Includes:

How to Qualify?

CNV Backbone Spike-in Panels

November 19, 2025/in News, NGS, Partners, Twist/by Harshita Sharma

Stronger CNV Detection — Without Changing Your Exome Workflow.

Large copy number variations can be easy to miss when exome sequencing focuses on exonic regions – leading to blind spots, repeat testing, and extra time interpreting unclear data. By spiking in Twist’s CNV Backbone Panels, you give your exome run the evenly spaced genomic coverage it needs to reliably surface clinically relevant CNVs — especially the ones standard exomes struggle with.

Available in 100 kb, 50 kb, and 25 kb resolutions, the CNV Backbone Panels strengthen your detection sensitivity while keeping your workflow identical. Blend it into your existing exome panel, follow your standard Twist enrichment protocol, and immediately get more confident CNV calls backed by consistent probe tiling across intergenic regions.

But... Why These Panels?

Download Poster on utilization of these panels with exome for cytogenetic research

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Why It Matters to You

Reliable CNV detection isn’t just a technical metric—it directly impacts research outcomes, diagnostic accuracy, and patient care. Standard exome sequencing often misses CNVs due to uneven probe coverage, creating blind spots in your analysis. Twist CNV Backbone Spike-in Panels bridge those gaps, ensuring that even subtle copy number changes are identified, so you can make confident, data-driven decisions.

For labs and clinicians, this means fewer follow-up tests, reduced time spent troubleshooting ambiguous results, and a smoother workflow. You can trust that your exome sequencing captures the variations that truly matter, whether for rare disease research, clinical diagnostics, or high-throughput screening.

Moreover, the ability to choose between 25 kb, 50 kb, or 100 kb resolution gives you control over sensitivity and throughput, aligning with your project goals and patient population needs. Evidence-based validation demonstrates improved detection of CNVs—including those smaller than 50 kb—so your results aren’t just comprehensive, they’re actionable.

By integrating these panels into your existing workflow, you enhance not only the quality of your data but also the efficiency of your lab operations, freeing time and resources for deeper analysis and patient-focused outcomes.

Select the CNV Resolution You Need

Table 1. Example data of Twist CNV Backbone Spike-in Panels. A highly characterized sample set known to contain CNVs (1) and a baseline set of 12 healthy individuals were sequenced with 2×150 reads on an Illumina NovaSeq 6000. The average number of SNVs, INDELs, and CNVs called and sequencing depth at each probe density was determined for each panel when spiked into Twist Exome 2.0 plus Comprehensive Spike-in. CNV calling was performed with a commercially available software solution (2)

(1) Coriell Institute’s CNVPANEL01 – Human CNV Reference Panel.
(2) eVai Platform (secondary workflow), enGenome Software.

A CRE.AI.TIVE application of AI: Engineering a more resilient global food supply

November 17, 2025/in News, Twist/by Harshita Sharma

A CRE.AI.TIVE application of AI: Engineering a more resilient global food supply

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Phytoform Labs harnessed its AI-powered CRE.AI.TIVE platform to develop climate-resilient crops, with a focus on drought-tolerant tomatoes. By rapidly exploring millions of potential sequence edits, the platform identified 2,000 high-potential candidates for wet-lab validation.

To overcome the challenge of synthesizing complex, AT-rich sequences with homopolymers, the team partnered with Twist Bioscience. Twist’s high-fidelity oligos ensured accurate transfer of AI-designed sequences to the lab, enabling efficient MPRA screening in tomato protoplasts.

This AI-guided workflow validated predictions while streamlining experiments—reducing waste, saving resources, and ensuring only the most promising variants progressed to in vivo testing.

Case Study Highlights

AI-driven design of millions of sequence variants
Efficient identification of high-impact edits, conserving time and resources
Ensuring fidelity of AI-generated oligos for complex plant sequences
Insights on impact and future directions

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.

Modified LongPlex™ Protocol (LongPlex XL)

November 17, 2025/in News, SeqWell/by Harshita Sharma

Modified LongPlex™ Protocol (LongPlex XL)

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This technical note outlines an alternative workflow for generating 10–15 kb HiFi reads from high-quality genomic DNA using the LongPlex Long Fragment Multiplexing Kit. In this approach, LongPlex is used to fragment and barcode samples, and PacBio’s Short Read Eliminator (SRE) is applied to size-select fragments >10 kb before SMRTbell® library preparation.

LongPlex uses plate-based transposase tagmentation for multiplexed fragmentation and barcoding, removing the need for mechanical shearing and allowing barcoded samples to be pooled before SMRTbell prep. This simplifies the workflow, increases throughput, and lowers library prep costs.

The standard LongPlex protocol generates 6–9 kb HiFi reads from high- to medium-quality DNA—ideal for microbial and other small-genome projects. However, users working with higher-quality DNA may want longer HiFi reads to maximize gigabase yield on PacBio systems.

This modified workflow is only suitable for high-quality DNA (Femto Pulse GQN30kb ≥7). Using degraded DNA will result in substantial sample loss during SRE size selection.

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.

Site Directed Mutagenesis

November 17, 2025/in Partners, Synbio Genes, Twist/by Harshita Sharma

Mutants Synthesized. Mutagenesis Simplified.

Make Site-Directed Mutagenesis precise, simple, and affordable with Twist’s Mutagenesis by Synthesis. Traditional site-directed mutagenesis can be time consuming and imprecise. Site directed mutagenesis through synthesis eliminates these complexities, providing you with precisely engineered sequences tailored to your exact specifications. From protein engineering to functional genomics, incorporate precision synthesis of mutants into your workflow and focus on achieving your research goals

Why it matters to you:

Precision engineering –

site-directed mutagenesis, custom DNA

Flexible design –

protein engineering, functional genomics

Fast turnaround –

Express Clonal Genes, rapid synthesis

Cost-effective –

affordable variants, scalable synthesis

How to Qualify

Product: Clonal Genes
Number of mutation per genes: No Limit
Mutation type: any number of point mutation,
deletions, and/or insertions*
Pricing: Discounts on every variant
(Please kindly contact your Decode Sales Rep for enquiry)

How it Works

Terms and Conditions
* This promo is only available to customers in the Asia Pacific region (excluding China and Japan). Pricing is subjected to changes.
* To enjoy the special service of site directed mutagenesis, please quote your previous order number or approach Decode Science support.
* Each mutation is defined as any combination of bases change within a 10 codon spread over the entire gene.
* Average turnaround time for Express Clonal Genes is 4 -7 business days. This time will vary based on complexity and length of the sequence. Orders placed outside of the US will incur additional delivery turnaround time. Turnaround time for Clonal Genes is subject to change based on customizations and complexity. Additional specification: 50ng – 2 ug.

Watch Successful Implementations

WEBINAR

Stronger, tighter, and faster: designing new protein functions

WEBINAR

Designing Enzymes for the Infinite Recycling and Upcycling of Plastic

WEBINAR

Screening Gene Libraries to Rapidly Identify Immune-recognised Virulence Genes.

As the authorized distributor of Twist Bioscience in Australia and New Zealand, Decode Science makes integrating Twist’s DNA synthesis solutions seamless. We connect your lab with high-throughput, high-fidelity Twist technology, enabling faster, more reliable genomic workflows—with local support and guidance every step of the way.

Twist Portfolio

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

November 13, 2025/in News, Parse/by Harshita Sharma

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

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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.

Optimized CRISPR/Cas9 Gene Knockout PDF

November 13, 2025/in EditCo, News, Partners/by Harshita Sharma

Accelerate knockout experiments with XDel’s next-generation CRISPR design.

EditCo Bio’s XDel technology eliminates the need for guide RNA pre-screening, using a coordinated multi-gRNA design that delivers consistently high on-target editing across immortalized, primary, and iPSC lines. Validated through 768 edited samples and 4,816 NGS libraries, XDel achieves robust knockout efficiency while minimizing off-target effects—saving time and improving reproducibility across diverse cell types.

Validated performance. Proven precision.
With a standardized amplicon sequencing QC workflow and high-throughput automation, XDel enables scalable, high-confidence Cas9-mediated editing for both pooled and single-cell clone analysis. Download the full guide to explore the data, workflows, and results behind EditCo Bio’s high-efficiency gene knockout strategy.

Unlock to Download Sheet

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.

Excel Sheet: STOmics Validated Tissue List

October 30, 2025/in News, STOmics/by Harshita Sharma

STOmics Validated Tissue List

Our STOmics validated tissue list provides researchers with a comprehensive reference of hundreds of tissue types successfully tested using Stereo-seq, the cutting-edge spatial transcriptomics technology. Each tissue entry includes detailed sample information, experimental parameters, and test results, allowing scientists to make informed decisions before starting their single-cell or spatial transcriptomics experiments. By consulting this list, you can ensure compatibility with your tissue samples and streamline your experimental design.

The list not only highlights tissue types that have been validated but also provides insights into the experimental conditions that yielded the most reliable results. Researchers can leverage this information to optimize sample preparation, sequencing protocols, and data quality control measures. This reduces trial-and-error, saves valuable time and resources, and ensures reproducibility across studies. It is an essential tool for anyone planning to use Stereo-seq for spatial gene expression profiling.

In addition, our STOmics validated tissue list supports better planning for large-scale studies and comparative analyses. By providing a centralized reference for tissue performance, it helps guide tissue selection, anticipate potential challenges, and maximize experimental success. Whether you are exploring new tissue types or scaling up existing workflows, this validated tissue list is your key resource for robust, high-quality spatial transcriptomics research.

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Notices:

The STOmics validated tissue list was generated using standard tissue and sample types, all of which are frozen. Each tissue sample had an area of less than 1 cm² and was sectioned at a thickness of 10 μm. Most experiments were performed using the Stereo-seq Transcriptomics Kit V1.2, with a few using V1.1. Sequencing depth ranged from 1–3 G reads per sample, and data were processed using the Stereo-seq Analysis Workflow (SAW) versions V2.1.0–V5.1.3. Testing was conducted between 2020 and 2022.

Please note that all test parameters and results are highly dependent on the tissue and sample type. This information should be used as a reference guide to help design and optimize your own experiments, rather than as definitive outcomes for all samples.

Key parameters included in the list:

MID (K): Bin200_Median_MID in thousands
GENETYPE (K): Bin200_Median_Genetype in thousands

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 News, Parse/by Harshita Sharma

Scale Single-Cell Research Like Never Before

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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.

Author Archive for: Harshita

About Harshita Sharma

Entries by Harshita Sharma

NGS Validation Package – Expert Support for Your Lab

Chris Wicky

Scott Coutts

Ain Roesley

1. Discover Cells in Their True Spatial Context

2. Multiplexed Protein and RNA Analysis

3. Actionable Insights Across the Research Continuum

4. Scalable, Reproducible Workflows

Module 1 - Consultancy Support

Module 2 - Wet Lab Validation Support

Module 3 - Dry Lab Validation Support

Proud Partnerships

How does it work?

Initiation

Assessment Phase

Support Plan Prep

We Work Together

we’re here to all your questions

Our team is one form away.

MosaiX High-Complexity Library Prep Kit , – Early Access Promotion

5/5

Chris Wicky

Early-Access Offer Includes:

How to Qualify?

Complete a short feedback survey by 31 December to access the early-bird discounted rate.

1. Fine-Tune CNV Resolution

2. Seamless Workflow Integration

3. Evidence-Based Performance

4. Flexible Panel Sizes

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Chris Wicky

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Chris Wicky

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Chris Wicky

Daina Elliott

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Dr. Ebru Boslem

Unlock to Download Sheet

Hamza Hassan

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Dr. Ebru Boslem

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Dr. Ebru Boslem

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Special October Offer

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NGS Validation Package
– Expert Support for Your Lab

MosaiX High-Complexity Library Prep Kit ,
– Early Access Promotion