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# new.alitheagenomics.com

## Sitemaps
[XML Sitemap](https://alitheagenomics.com/sitemap_index.xml): Includes all crawlable and indexable pages.

## Posts
- [Webinar: AI-ready ultra-high-throughput whole transcriptome profiling with MERCURIUS™ 1536 DRUG-seq](https://alitheagenomics.com/webinar-ai-ready-ultra-high-throughput-whole-transcriptome-profiling-with-mercurius-1536-drug-seq/): For the first time, 1536-well whole transcriptome profiling brings biologically rich readouts to primary screening and large-scale perturbation dataset generation.
- [Alithea Genomics Launches Early Access Program for MERCURIUS™ 1536 DRUG-seq, Bringing Transcriptomics to Compound Screening Scale](https://alitheagenomics.com/alithea-genomics-launches-early-access-program-for-mercurius-1536-drug-seq-bringing-transcriptomics-to-compound-screening-scale/): LAUSANNE, Switzerland and FREDERICK, Md., USA, June 15, 2026 – Alithea Genomics today announced the early access launch of MERCURIUS™ 1536 DRUG-seq, a new ultra-high-throughput transcriptomics kit designed to help drug discovery teams profile compound-induced biological responses at true screening scale.
- [Alithea Genomics and Revvity announce distribution agreement to expand access to MERCURIUS™ DRUG-seq solutions](https://alitheagenomics.com/alithea-genomics-and-revvity-announce-distribution-agreement-to-expand-access-to-mercurius-drug-seq-solutions/): June 8, 2026
- [High-Throughput Transcriptomic Biomarker and Mechanism of Action Discovery: From Gene Expression Signatures to Clinical Outcomes](https://alitheagenomics.com/high-throughput-transcriptomic-biomarker-and-mechanism-of-action-discovery-from-gene-expression-signatures-to-clinical-outcomes/): Biomarker discovery is nothing new. However, classical single-endpoint biomarkers, like serological or biochemical indicators, often provide only limited specificity and predictive capacity. In contrast, transcriptome-wide, systems-level gene expression biomarkers offer researchers greater predictive power for earlier detection of safety concerns or responses to drugs (2). Multi-dimensional transcriptomic biomarkers also inform numerous aspects of biology, including disease pathways, progression, and mechanisms of action.  
- [How High-Throughput Transcriptomics Solves the AI Training Data Bottleneck in Drug Discovery ](https://alitheagenomics.com/how-high-throughput-transcriptomics-solves-the-ai-training-data-bottleneck-in-drug-discovery/): Traditional RNA-seq workflows require RNA extraction, individual-sample library preparation, and per-sample handling in separate tubes. These stages, especially RNA extraction, are far too slow for industrial-scale screening and for generating AI training data of sufficient size (18). Similarly, these excessive processing steps make scaling to hundreds of thousands or millions of samples prohibitively costly. Traditional RNA-seq ultimately creates datasets that are far too small to train generalizable models. 
- [SOT Annual Meeting and ToxExpo 2026: Key Themes in Omics-Driven Mechanistic Toxicology to Watch](https://alitheagenomics.com/sot-annual-meeting-and-toxexpo-2026-key-themes-in-omics-driven-mechanistic-toxicology-to-watch/): As the SOT Annual Meeting and ToxExpo 2026 approaches, we take a pre-conference look at the program through a transcriptomics-focused lens. One overall shift is clear: toxicology is moving from descriptive apical observation toward predictive, mechanism-driven safety science. Across the program, many sessions highlight how transcriptomics and other omics technologies are enabling toxicologists
- [Alithea Genomics Closes CHF 6.9M Seed Round, Using Proceeds to Unlock Industrial-Scale RNA-seq for Primary Drug Screening and Toxicology](https://alitheagenomics.com/alithea-genomics-closes-chf-6-9-m-seed-round-using-proceeds-to-unlock-industrial-scale-rna-seq-for-primary-drug-screening-and-toxicology/): LAUSANNE, Switzerland--(BUSINESS WIRE)--Alithea Genomics, an emerging leader in the field of large-scale RNA sequencing and transcriptomics, announced today the closing of its seed financing round with an additional CHF 3 million ($3.9 million), led by Genku Ventures and joined by Novalis Biotech and Zürcher Kantonalbank as well as several private investors. This additional funding brings the total seed round to CHF 6.9 million ($8.9 million). The proceeds will be used primarily to accelerate commercialization of its new 1536‑well MERCURIUSTM DRUG-seq kits unlocking greater potential of using cell transcriptomics in primary drug screening and exploratory toxicology. These applications, previously out of reach due to cost and throughput constraints, can now be addressed by scaling 3′RNA‑seq library preparation to 1,536 samples. Alithea will also invest the proceeds in accelerating new technology development and building proprietary transcriptomic data assets to fuel the industry's AI/ML initiatives.
- [Case Study: Combining High-Content Imaging and MERCURIUS™ DRUG-seq to Identify Brain-Penetrant Modulators of Microglial Function ](https://alitheagenomics.com/case-study-combining-high-content-imaging-and-mercurius-drug-seq-to-identify-brain-penetrant-modulators-of-microglial-function/): Identifying brain-penetrant small-molecule modulators of human microglia using a cellular model of synaptic pruning - McCrea and Batorsky et al.  
- [Published DRUG-seq vs MERCURIUS™ DRUG-seq: Key Differences Explained ](https://alitheagenomics.com/published-drug-seq-vs-mercurius-drug-seq-key-differences-explained/): DRUG-seq, first published in 2018, has transformed how pharmaceutical, cosmetics, agritech, and AI drug discovery companies screen compounds for on- and off-target effects, mechanisms of action, drug repurposing, and toxicology (1, 2). By moving beyond narrow gene panels and their associated biases toward scalable and affordable transcriptome-wide data, DRUG-seq looks set to improve decision-making capabilities, strengthen early pipelines, and boost compound safety and success rates in the clinic.  
- [DRUG-seq for CRISPR screens](https://alitheagenomics.com/drug-seq-for-crispr-screens/): In recent years, the convergence of CRISPR gene editing and high-throughput screening methodologies has revolutionized genomic research. While the toolkits to edit individual genes have been rapidly developed, the large-scale screening methods based on the edited gene have gained attention in the past 10 years1,2,3.  Integrating CRISPR with high-throughput screening merges the precision of genome editing with large-scale screening, making it possible to rapidly identify and validate biological targets, pathways, and therapies systematically and efficiently. 
- [TempO-seq™ for High-Throughput Toxicology: A Case Study](https://alitheagenomics.com/tempo-seq-for-high-throughput-toxicology-a-case-study/): As a researcher performing large-scale drug-discovery, genetic perturbation, or toxicogenomic screens, probe-based targeted gene expression profiling assays like Templated Oligo assay with Sequencing (TempO-seq™) from BioSpyder™ are often a suitable choice thanks to their high throughput, targeted, and relatively cost-effective nature compared to traditional RNA-seq approaches.
- [Tackling Plastic Waste and CO2 Emissions for Pharma Sustainability: Does Massive Sample Multiplexing Offer a Path to Lab Sustainability? ](https://alitheagenomics.com/tackling-plastic-waste-and-co2-emissions-for-pharma-sustainability-does-massive-sample-multiplexing-offer-a-path-to-lab-sustainability/): Summary: Life science labs are major CO2 emitters due to plastic use, hindering lab sustainability efforts. New massively multiplexed transcriptomic workflows, such as MERCURIUS™ DRUG-seq, can cut plastic consumption by up to 95% according to internal estimates, lowering waste, emissions, and costs while maintaining data quality and helping achieve pharma sustainability.
- [The OASIS Consortium: Can Multi-Omics Improve Chemical Safety Assessment?](https://alitheagenomics.com/the-oasis-consortium-can-multi-omics-improve-chemical-safety-assessment/): Summary - How is Multi-Omics Changing Toxicology? 
- [SPT Labtech and Alithea Genomics Collaborate to Automate Ultra Sensitive Single-Cell Transcriptomic Workflows](https://alitheagenomics.com/spt-labtech-and-alithea-genomics-collaborate-to-automate-ultra-sensitive-single-cell-transcriptomic-workflows/): Cambridge, UK, and Lausanne, Switzerland, 05 November 2025: SPT Labtech, a global leader in the design and development of laboratory automation and liquid handling solutions, and Alithea Genomics, a pioneer in the field of large-scale RNA sequencing and transcriptomics, today announced a collaboration to provide an automated solution for single-cell transcriptomics.
- [Alithea Genomics Introduces MERCURIUS™ Spheroid DRUG-seq: Extraction-Free, RNA-seq for 3D Drug Screening and Toxicology](https://alitheagenomics.com/alithea-genomics-introduces-mercurius-spheroid-drug-seq-extraction-free-rna-seq-for-3d-drug-screening-and-toxicology/): Lausanne, Switzerland and Frederick, MD – September 25, 2025 – Alithea Genomics, a leader in next-generation transcriptomic solutions, today announced the commercial launch of MERCURIUS™ Spheroid DRUG-seq, a novel, extraction-free RNA sequencing library preparation kit built for 3D spheroid models. This advancement extends Alithea’s MERCURIUSTM DRUG-seq technology into physiologically relevant 3D systems, bringing simplicity, sensitivity, and throughput to drug screening in more in vivo–like cellular environments.
- [Omics in Short-Term Toxicology Studies: Are We Ready to Replace Traditional Approaches?](https://alitheagenomics.com/omics-in-short-term-toxicology-studies-are-we-ready-to-replace-traditional-approaches/): Toxicology is at a turning point. For decades, decision-making relied on long-term animal studies, which included 90-day or even 2-year rodent trials, to identify adverse effects, set exposure limits, and protect human health. But these studies are costly, slow, and increasingly misaligned with today’s push for human-relevant, mechanism-based safety evaluations that minimize animal use and maximize compound success. 
- [MERCURIUS™ FLASH-seq vs 10x Genomics Chromium: Which Single-Cell RNA-seq Approach is Right for You? ](https://alitheagenomics.com/mercurius-flash-seq-vs-10x-genomics-chromium-which-single-cell-rna-seq-approach-is-right-for-you/): Single-cell RNA sequencing (scRNA-seq) has revolutionized our ability to examine the cellular heterogeneity of complex samples, identify new cell types, and explore transcriptional regulation at unprecedented resolution. But not all scRNA-seq methods are created equal, and the right choice depends heavily on your biological question, sample type, and experimental design.  
- [Opportunities and Challenges of the Connectivity Map and L1000](https://alitheagenomics.com/opportunities-and-challenges-of-the-connectivity-map-and-l1000-gene-expression-profiling/): High-throughput gene profiling and drug screening projects have generated vast amounts of biological data, giving researchers endless opportunities to untangle complicated biological questions.
- [How Does RASL-seq Compare to  BRB-seq and DRUG-seq](https://alitheagenomics.com/the-strengths-and-weaknesses-of-rasl-seq-compared-to-mercurius-brb-seq-and-mercurius-drug-seq/): Determining the most suitable transcriptomic technology to drive your large-scale compound screen, clinical study, or to assess a panel of genetic perturbations can be a headache, especially if you’re unfamiliar with the strengths and limitations of various sequencing technologies.
- [What does ‘high-throughput’ mean in sequencing?](https://alitheagenomics.com/what-does-high-throughput-mean-in-sequencing/): High-throughput’ in sequencing refers to the amount of DNA molecules read at the same time. Technologies are now capable of sequencing many fragments of DNA in parallel. This enables scientists to read hundreds of millions of DNA fragments and generate more data, with less time and costs than ever before.
- [What is Bulk RNA Sequencing (Bulk RNA-seq)?](https://alitheagenomics.com/bulk-rna-seq/): Bulk RNA Sequencing: A Gateway to Comprehensive Transcriptomics
- [TempO-seq VS MERCURIUS™ DRUG-seq in Compound Screening ](https://alitheagenomics.com/tempo-seq-vs-drug-seq-in-compound-screening/): Understanding the transcriptomic impacts of new compounds on cells is essential in drug development and toxicology. This process helps researchers evaluate a drug's on- or off-target effects, its toxicity, and potential mechanisms of action. Such insights are crucial for determining the safety and effectiveness of new therapeutic candidates. 
- [What is the difference between Smart-seq2, Smart-seq3, and FLASH-seq for full-length single-cell RNA-seq?  ](https://alitheagenomics.com/what-is-the-difference-between-smart-seq2-smart-seq3-and-flash-seq-for-full-length-single-cell-rna-seq/): The Smart-seq2 protocol was the gold standard for full-length plate-based single-cell RNA-seq, offering superior sensitivity and the transcript coverage necessary to detect splice isoforms, allelic variants, and single-nucleotide polymorphisms (SNPs) compared to droplet-based methods (1-3). 
- [How to Choose the Right RNA-seq Service Provider for Your Screening Study](https://alitheagenomics.com/how-to-choose-the-right-rna-seq-service-provider-for-your-screening-study/): For biotech and pharma teams under pressure to deliver actionable results for investors or to reach drug discovery milestones, outsourcing your transcriptomic screens to an RNA-seq service provider is a smart strategic decision that can accelerate every stage of the pipeline.
- [Questions About our RNA-Seq Service? Look No Further!](https://alitheagenomics.com/questions-about-our-rna-seq-service-look-no-further/): If you’re considering using our RNA-seq service for your high-throughput screen, we want to make the process as straightforward and streamlined as possible for you. 
- [Alithea Genomics Announces the Launch of MERCURIUS™ FLASH-seq: A Plate-Based, Full-Length Single Cell RNA-seq Kit Delivering Exceptional Sensitivity and Simplicity](https://alitheagenomics.com/alithea-genomics-announces-the-launch-of-mercurius-flash-seq-a-plate-based-full-length-single-cell-rna-seq-kit-delivering-exceptional-sensitivity-and-simplicity/): Lausanne, Switzerland and Frederick, MD – June 19, 2025 – Alithea Genomics, a pioneering biotech company based in Switzerland and the USA specializing in high-throughput RNA sequencing solutions, today announced the commercial launch of MERCURIUS™ FLASH-seq, a next-generation library preparation kit for full-length single-cell RNA sequencing.
- [Alithea Genomics Launches MERCURIUS™ Total DRUG-seq: A Next-Generation Full-Length Transcriptome Profiling Platform for High-Throughput Compound Screening and Target Validation](https://alitheagenomics.com/alithea-genomics-launches-mercurius-total-drug-seq-a-next-generation-full-length-transcriptome-profiling-platform-for-high-throughput-compound-screening-and-target-validation/): Lausanne, Switzerland and Frederick, MD – June 19, 2025 – Alithea Genomics, a pioneering biotech company based in Switzerland and the USA specializing in scalable RNA sequencing solutions, today announced the launch of MERCURIUS™ Total DRUG-seq, a new extraction-free, full-length transcriptome profiling library preparation kit designed to push the boundaries of high-throughput drug screens, toxicology screens and target validation by enabling the creation of large-scale data generation for machine learning and AI.
- [TaqMan Gene Expression Assays for Compound Screening. Time for an Omics Upgrade?](https://alitheagenomics.com/taqman-gene-expression-assays-for-compound-screening-time-for-an-omics-upgrade/): Since their development around 30 years ago, TaqMan™ gene expression assays have been a popular choice for scientists requiring highly sensitive and specific readouts of gene activity.
- [What are TaqMan Gene Expression Assays?](https://alitheagenomics.com/what-are-taqman-gene-expression-assays/): Accurately measuring gene expression is fundamental to modern drug discovery and development, enabling researchers to evaluate cellular responses to potential therapeutic compounds. One of the widely used technologies for this purpose is the TaqMan™ gene expression assay, a real-time PCR-based method that offers high sensitivity, specificity, and reproducibility.
- [Designing Successful RNA-Seq Experiments for Drug Discovery: A Strategic Approach](https://alitheagenomics.com/designing-successful-rna-seq-experiments-for-drug-discovery-a-strategic-approach/): Choosing the right RNA-seq library preparation strategy is key to unlocking meaningful transcriptomic insights in drug discovery projects that don’t break the bank. Whether it's target identification, biomarker discovery, or transcriptome profiling, your experiment’s goals should directly inform the design of your wet lab workflow.
- [ Overview of Published 3’ mRNA-seq Workflows: From Early Multiplexing and Beyond](https://alitheagenomics.com/overview-of-published-3-mrna-seq-workflows-from-early-multiplexing-and-beyond/): With a growing number of published 3’ mRNA-seq methods now available, researchers have more choices than ever for high-throughput and cost-effective transcriptomic screening. While broadly similar, 3’ mRNA-seq protocols often differ in how they barcode and multiplex samples, synthesize cDNA, and prepare libraries, which can impact cost, throughput, and data quality.
- [BRB-seq pipeline – downstream analysis best practices](https://alitheagenomics.com/brb-seq-pipeline-downstream-analysis-best-practices/): In this post, we will see briefly how to perform downstream analysis for RNA-seq data.
- [Published Bulk 3’ mRNA-seq Technologies: Which is Best for Your Next Screen?](https://alitheagenomics.com/published-bulk-3-mrna-seq-technologies-which-is-best-for-your-next-screen/): 3’ mRNA-seq technologies are gradually revolutionizing high-throughput bulk transcriptomics.
- [Maximizing Drug Discovery with High-Throughput and High-Content Screening](https://alitheagenomics.com/maximizing-drug-discovery-with-high-throughput-and-high-content-screening/): High-throughput screening and high-content screening are foundational to the early stages of drug discovery and development pipelines. The pharmaceutical industry harnesses both approaches to sift through vast libraries of compounds or genetic perturbations in parallel to identify promising therapeutic candidates, study diverse biological systems, and identify potential molecular targets, pathways, and cytotoxic effects crucial for downstream decision making.
- [High-content screening in drug discovery: A brief guide](https://alitheagenomics.com/high-content-screening-in-drug-discovery-a-brief-guide/): High-content screening is a powerful quantitative image-based approach that has transformed drug discovery, from target identification and primary compound screening to mechanism-of-action studies and in vitro toxicology.
- [How can pairing the JUMP-Cell Painting Gallery with MERCURIUS™ DRUG-seq help your large-scale drug discovery or toxicology study?](https://alitheagenomics.com/how-can-pairing-the-jump-cell-painting-gallery-with-mercurius-drug-seq-help-your-large-scale-drug-discovery-or-toxicology-study/): For researchers in pharma, biotech, or academia looking to uncover the mechanisms of action, cytotoxicity, or possible on- and off-target effects of drugs in their development pipeline or potential genes of interest, JUMP-CP is an impressive publicly available resource that acts as a great starting point.
- [Missed Toxicity Signals? Unclear Mechanisms of Action? Can MERCURIUS™ DRUG-seq and Cell Painting De-Risk Drug Discovery?](https://alitheagenomics.com/missed-toxicity-signals-unclear-mechanisms-of-action-can-mercurius-drug-seq-and-cell-painting-de-risk-drug-discovery/): For researchers performing drug discovery, drug repurposing, toxicogenomic screens, or CRISPR screens, the end goal is often to uncover mechanisms of action, determine on- and off-target effects, establish the presence of cytotoxicity, or discover entirely new leads for exploration in preclinical phases.
- [What is JUMP-CP consortium?](https://alitheagenomics.com/what-is-jump-cp-consortium/): The Joint Undertaking in Morphological Profiling-Cell Painting Gallery (JUMP-CP) is a large-scale, high-content imaging reference dataset created with the Cell Painting technology that assesses the morphological effects of tens of thousands of drug and genetic perturbations on cells.
- [Can Combining Cell Painting and L1000 Accelerate Drug Discovery?](https://alitheagenomics.com/can-combining-cell-painting-and-l1000-accelerate-drug-discovery/): Large-scale perturbational profiling is time and cost-intensive, so it’s crucial to compare the capabilities of different technologies to help plan and design experiments efficiently.
- [What is Cell Painting?](https://alitheagenomics.com/what-is-cell-painting/): Imagine if cells could attend an art class. Instead of brushes and canvases, they'd use fluorescent dyes and high-throughput microscopes to create their own masterpieces. Welcome to the world of Cell Painting, where biology meets art in the most colorful way possible! This innovative technique doesn't just make pretty pictures; it reveals the hidden secrets of cellular life by highlighting key components and organelles.
- [What is DRUG-seq and What Are Its Benefits in Drug Discovery?](https://alitheagenomics.com/what-is-drug-seq-and-what-are-its-benefits-in-drug-discovery/): DRUG-seq is a cost-effective, high-throughput bulk RNA-seq library preparation method for compound screening in drug discovery and development (Ye et al., 2018; Li et al., 2022). Digital RNA with pertUrbation of Genes (DRUG-seq) provides sensitive, unbiased gene expression readouts across the whole transcriptome and is built for the data-driven, AI-aided discovery era.  
- [BRB-seq for large scale crop science projects](https://alitheagenomics.com/brb-seq-for-large-scale-crop-science-projects/): The world of crop science is evolving rapidly. New technologies are emerging that promise to revolutionize the field. One such technology is BRB-seq.
- [Using External RNA Controls Consortium (ERCC) Molecules Enhances Quality Controls and Biological Interpretation in MERCURIUS™ DRUG-seq](https://alitheagenomics.com/using-external-rna-controls-consortium-ercc-molecules-enhances-quality-controls-and-biological-interpretation-in-mercurius-drug-seq/): MERCURIUS™ DRUG-seq is a rapid, cost-effective, RNA-extraction-free bulk 3’ mRNA-seq method. It provides ultra-high-throughput studies, such as drug discovery and toxicogenomic screens, with unbiased, transcriptome-wide gene expression data for hundreds of compounds or experimental conditions simultaneously. Featuring early sample barcoding technology, MERCURIUS™ DRUG-seq kits enable a single next-generation sequencing (NGS) lab technician to generate sequencing libraries from up to 5000-10’000 cells per well in 384 plates in less than two days without relying on any devoted automation. MERCURIUS™ DRUG-seq delivers accurate and reproducible transcriptomic read-outs for typically over 16,000 genes at a sequencing depth of one million reads per sample.
- [How PAXgene® and Tempus™ blood tubes influence RNA expression signatures](https://alitheagenomics.com/how-paxgene-and-tempus-blood-tubes-influence-rna-expression-signatures/): RNA expression signatures are essential for understanding the molecular mechanisms underlying many biological processes and diseases. The analysis of RNA expression signatures provides information about the gene expression levels in a sample and can reveal key insights into the function of different genes, pathways, and biological processes. However, the quality and stability of the RNA in a blood sample can be greatly influenced by the way that the sample is collected, stored, and processed for RNA library preparation. This is where PAXgene® (PreAnalytiX) and Tempus™ (Applied Biosystems) blood tubes come into play.
- [What is the Connectivity Map and how can it accelerate drug discovery?](https://alitheagenomics.com/what-is-the-connectivity-map-and-how-can-it-accelerate-drug-discovery/): The Connectivity Map is a large-scale comprehensive catalog of cellular transcriptomic signatures that represent systematic genetic or pharmacologic perturbations of many human disease cell types (Lamb et al., 2006; Subramanian et al., 2017).
- [Functional drug screening: microarray vs RNA-seq](https://alitheagenomics.com/functional-drug-screening-microarray-vs-rna-seq/): RNA-seq, in contrast, offers the opportunity to interrogate the entire transcriptome at a given moment at single-base resolution without prior knowledge of genes that might be impacted by a particular treatment or condition, thus providing a more comprehensive, hypothesis-free view of the transcriptome.
- [Blood transcriptomics: sequence deeper or sequence more samples?](https://alitheagenomics.com/blood-transcriptomics-sequence-deeper-or-sequence-more-samples/): Expression Quantitative Trait Loci (eQTLs) in large-scale RNA-seq studies are of great medical interest as they can be employed to understand functional consequences of genetic variants and to personalize and adjust in real-time disease therapy.
- [Whole blood RNA-seq to guide COVID-19 treatment](https://alitheagenomics.com/whole-blood-rna-seq-to-guide-covid-19-treatment/): Currently, there is no efficient way to predict how the immune system will respond to COVID-19 exposure. The immune response could range from mild symptoms, all the way to severe symptoms, which can lead to, unfortunately, intensive care unit or even death.
- [A story of fruit flies, sleep and RNA-seq](https://alitheagenomics.com/a-story-of-fruit-flies-sleep-and-rna-seq/): Sharing around 60% of human DNA, the humble insect has been the linchpin of countless scientific discoveries, from genetic inheritance and gene mutation to neurodegenerative disorders like Alzheimer’s and Parkinson’s.
- [Single and bulk RNA-seq working together to boost immuno-oncology](https://alitheagenomics.com/single-and-bulk-rna-seq-working-together-to-boost-immuno-oncology/): Immunotherapy itself is an approach that aims at using or re-purposing a patient's immune system to fight back cancer.
- [What is BRB-seq?](https://alitheagenomics.com/what-is-brb-seq/): Bulk RNA barcoding and sequencing (BRB-seq) is an innovative, efficient, and cost-effective RNA sequencing technology that leverages the benefits method of early-stage barcoding and unique molecular identifiers (UMIs) to produce consistent, reproducible, and uniform RNA sequencing data (Alpern et al. 2019). Despite the utility of RNA sequencing (RNA-seq) in transcriptomics, traditional RNA-seq technologies are still too time consuming, costly, and analytically challenging to replace reverse transcription-quantitative real-time PCR (qRT-PCR) as the preferred method of quantifying changes in gene expression. In contrast, BRB-seq generates high-quality transcriptomic data with mere hours of hands-on time at a cost tantamount to profiling four individual genes using conventional qRT-PCR (Alpern et al. 2019).
- [BRB-seq vs Truseq](https://alitheagenomics.com/brb-seq-vs-truseq/): Currently, the de facto standard workflow for bulk transcriptomics is the directional dUTP approach and its commercial adaptation “Illumina TruSeq Stranded mRNA”. However, like most current RNA-seq protocols, TruSeq relies on late multiplexing, which necessitates the processing of samples on a one-by-one basis. To overcome this limitation, BRB-seq uses early multiplexing to produce 3′ cDNA libraries, which provides great capacity for transforming large sets of samples into a unique sequencing library. This allows to process thousands of samples by combining the sample barcode indexing with the library indexing, which makes the design of the project very flexible. Moreover, it simplifies a lot the handling of the samples, which not only reduce the hands-on time, but also reduce cost significatively, and thus provide a much cheaper solution per sample than what TruSeq can offer.
- [How do BRB-seq pre-processing results look like?](https://alitheagenomics.com/how-do-brb-seq-pre-processing-results-look-like/): BRB-seq libraries should be composed of a pair of .fastq files (mylibrary_R1.fastq.gz and mylibrary_R2.fastq.gz) after Illumina sequencing and standard index demultiplexing.
- [COVID-19 under the BRB-Seq microscope: A Tale of Two Coronaviruses](https://alitheagenomics.com/covid-19-under-the-brb-seq-microscope-a-tale-of-two-coronaviruses/): RNA sequencing (RNA-seq) provides a molecular snapshot of the cellular transcriptome, offering a treasure trove of information regarding gene regulation and expression. One of the most common—and arguably the most biologically relevant—applications of RNA sequencing is the ability to assess differential gene expression (DGE), which provides invaluable data on genome-wide differences in gene expression between biological samples. As changes in gene expression often involve multiple comparisons—such as between wild types and mutants, life history stages, experimental time points, or environmental conditions—and normally include controls and replicates, DGE analyses often involve numerous RNA samples. However, until recently, traditional RNA-seq strategies have been too laborious, expensive, and analytically challenging to replace reverse transcription-quantitative real-time PCR (qRT-PCR) as the preferred method of quantifying changes in gene expression, thereby limiting the number of RNA samples that can be processed (Alpern et al. 2019).
- [Large-scale RNA-seq series – Ep.1: RNA-seq helps uncover the genetic regulation of blood cells](https://alitheagenomics.com/ht-transcriptomics-ep-1-large-scale-rna-seq-helps-uncover-the-genetic-regulation-of-blood-cells/): The largest blood cell genotyping and transcriptomic study ever performed has shown that a much higher number of common changes in the DNA sequence affect gene expression in blood cells than previously thought (Võsa et al. 2021). In this article, we look at how the use of RNA-seq in this study contributed to these exciting new discoveries in the genetic regulation of blood cells.
- [Large-scale RNA-seq series – Ep.2: Predicting cancer outcomes by estimation of tumor specific total mRNA levels in bulk RNA-seq](https://alitheagenomics.com/large-scale-rna-seq-series-ep-2-predicting-cancer-outcomes-by-estimation-of-tumor-specific-total-mrna-levels-in-bulk-rna-seq/): A recent ground-breaking study uses a mathematical approach to measure tumor-specific total mRNA levels from mixed tumor samples. Bulk RNA-seq data from 6,664 tumor samples and 15 different cancers show that reduced patient survival is associated with higher total mRNA levels in cancer cells (Cao et al. 2022).
- [BRB-seq in cancer therapeutics: differential gene expression elucidates the molecular mechanisms of high-grade pediatric gliomas](https://alitheagenomics.com/brb-seq-in-cancer-therapeutics-differential-gene-expression-elucidates-the-molecular-mechanisms-of-high-grade-pediatric-gliomas/): Diffuse midline gliomas: background and emerging therapies
- [Large-scale RNA-seq series Ep. 4: BRB-seq uncovers novel features of fruit fly embryogenesis](https://alitheagenomics.com/large-scale-rna-seq-series-ep-4-brb-seq-uncovers-novel-features-of-fruit-fly-embryogenesis/): A recent publication has used Bulk RNA Barcoding and sequencing (BRB-seq) to investigate one of the fundamental questions of embryonic development (Liu et al., 2020).
- [Large-scale RNA-seq series – EP.3: ‘Multi-omics’ improves the classification of 33 different cancer types using 10,000 tumor samples.](https://alitheagenomics.com/large-scale-rna-seq-series-ep-3-multi-omics-improves-the-classification-of-33-different-cancer-types-using-10000-tumor-samples/): In 2018 The Cancer Genome Atlas (TCGA) published groundbreaking findings from the largest ‘multi-omics’ cancer study ever performed (Hoadley et al., 2018).
- [Large-scale RNA-seq series – Ep. 5. – Gene expression networks control organ development across species](https://alitheagenomics.com/large-scale-rna-seq-series-ep-5-gene-expression-networks-control-organ-development-across-species/): In one of the largest studies of its kind, researchers used bulk RNA-seq to decode the gene expression landscape of development. The study focused on seven organs from seven different species, before and after birth (Cardoso-Moreira et al., 2019).
- [Large-scale RNA-seq series Ep. 6 – Sex Impacts Gene Expression, but not the way you think!](https://alitheagenomics.com/large-scale-rna-seq-series-ep-6-sex-impacts-gene-expression-but-not-the-way-you-think/): In 2020, the Genotype-Tissue Expression (GTEx) Consortium published seminal findings about how sex influences tissue-specific gene expression (Oliva et al., 2020). Using large scale RNA-seq they found that over one third of all human genes have differences in gene expression depending on sex in at least one type of tissue.
- [How does BRB-seq compare to SCRB-seq?](https://alitheagenomics.com/how-does-brb-seq-compare-to-scrb-seq/): Novel sequencing technologies based on the 3' barcoding of mRNA now enable transcriptomic studies with higher sample numbers and lower costs than ever before.
- [Budgeting for an mRNA-seq project? Here are the main cost drivers to keep an eye on.](https://alitheagenomics.com/budgeting-for-an-mrna-seq-project-here-are-the-main-cost-drivers-to-keep-an-eye-on/): The cost of RNA-sequencing (RNA-seq) ranges from approximately $36.9 to $173 for a single sample in an mRNA-seq experiment. Sequencing costs have dropped significantly thanks to the ‘multiplexing’ of hundreds of samples in one sequencing run. The most expensive step is now often the library preparation; however, 3’ mRNA-seq barcoding and pooling library preparation methods are reducing these costs dramatically (Figure 1). Despite this, the true cost still depends on your experimental question.
- [DRUG-seq: A Validated Method For Drug Discovery](https://alitheagenomics.com/drug-seq-a-validated-method-for-drug-discovery/): DRUG-seq is a novel high-throughput, cost-effective RNA-seq method for drug discovery (Ye et al., 2018; Li et al., 2022). Researchers have used DRUG-seq and similar techniques for compound screening applications in many disease areas. Like all novel methods, high-throughput sequencing techniques require extensive validation before use at scale.
- [Three New High-Throughput Transcriptomic Technologies for Drug Discovery](https://alitheagenomics.com/three-new-high-throughput-transcriptomic-technologies-for-drug-discovery/): DRUG-seq, Combi-seq, and BRB-seq are three novel high-throughput transcriptomic technologies accelerating drug discovery in more disease areas than ever before. They provide unbiased, comprehensive gene expression data after treatment with large compound libraries, under multiple experimental conditions, at significantly lower costs than traditional RNA-seq methods.
- [Cost-effective 3’ mRNA-seq technologies: How similar are they?](https://alitheagenomics.com/cost-effective-3-mrna-seq-technologies-how-similar-are-they/): Novel, high-throughput 3’ mRNA-seq technologies are driving cost-efficient, transcriptomic experiments at a larger-scale than ever before. Numerous 3’ mRNA-seq options are now available, such as the MERCURIUS™ BRB-seq kit from Alithea Genomics, QuantSeq-Pool from Lexogen, and the QIAseq UPX 3’ transcriptome kit from QIAGEN.
- [What is High-Throughput RNA-Sequencing?](https://alitheagenomics.com/what-is-high-throughput-rna-sequencing/): High-throughput RNA-sequencing (RNA-seq) is the use of next generation sequencing technology to explore the transcriptome of a genome. It allows researchers to characterize and compare gene expression profiles of biological samples. RNA-seq is now one of the most common tools in molecular biology.
- [What is high-throughput gene expression detection?](https://alitheagenomics.com/what-is-high-throughput-detection-of-gene-expression/): What Is High-Throughput Detection of Gene Expression?
- [Examples of High-Throughput RNA-seq Technologies](https://alitheagenomics.com/examples-of-high-throughput-rna-seq-technologies/): Novel, high-throughput 3’ mRNA-seq technologies like MERCURIUS™ BRB-seq from Alithea Genomics and the QuantSeq-Pool and QuantSeq 3’ mRNA-seq library prep kits from Lexogen are driving cost-efficient, transcriptomic experiments at a larger-scale than ever before.
- [What Is Whole Blood Transcriptome?](https://alitheagenomics.com/what-is-whole-blood-transcriptome/): Whole blood transcriptome refers to the genome-wide expression of all genes from cells contained in the blood. The transcriptomic analysis of whole blood has the potential to revolutionize non-invasive diagnostic identification of diseases as it provides a comprehensive gene expression profile of an organism’s physiological state.
- [What Is Blood Transcriptome Sequencing?](https://alitheagenomics.com/what-is-blood-transcriptome-sequencing/): Blood transcriptome sequencing is an RNA-seq based technology that investigates the expression level of all mRNA transcripts contained in the blood. Blood transcriptomic technologies block highly expressed hemoglobin mRNA transcripts before sequencing to provide more accurate and unbiased readouts. This sets it apart from standard RNA-seq techniques.
- [Whole Blood Transcriptome Sequencing With RNA-seq](https://alitheagenomics.com/whole-blood-transcriptome-sequencing-with-rna-seq/): Novel technologies based on RNA-sequencing (RNA-seq) are now streamlined to sequence hundreds of whole blood transcriptomes simultaneously. These ‘ultra-high-throughput’ RNA-seq technologies generate high-quality transcriptional information at low-cost. Therefore, they have the potential to revolutionize both large-scale investigative studies and non-invasive, blood-based diagnostic identification of diseases.
- [How to Preserve RNA Quality in Whole Blood Samples](https://alitheagenomics.com/how-to-preserve-rna-quality-in-whole-blood-samples/): Whole blood is one of the most routinely used sample types for RNA isolation and sequencing. This is largely thanks to its accessibility. New RNA-seq methods now allow researchers and clinicians to use whole blood transcriptomes for disease diagnosis, continual monitoring and prognosis (Frésard et al., 2019).
- [Benefits of Blood BRB-seq](https://alitheagenomics.com/benefits-of-blood-brb-seq/): Ultra-high-throughput whole blood Bulk RNA Barcoding and Sequencing from Alithea Genomics (MERCURIUS™ Blood BRB-seq) provides researchers and companies with numerous benefits compared to traditional blood RNA-seq approaches.
- [Benchmarking Blood BRB-seq and GLOBINclear™](https://alitheagenomics.com/benchmarking-blood-brb-seq-and-globinclear/): Whole blood RNA samples contain high levels of globin RNAs which reduce the sensitivity to detect genes from the rest of the blood transcriptome (Debey et al., 2006; Shin et al., 2014). Numerous globin depletion methods have been developed to block these transcripts before RNA-seq library preparation and sequencing (Jang et al., 2020). This ensures maximum sensitivity to detect relevant and interesting gene candidates.
- [RNA Preservation Methods to Improve RNA Quality and Quantity](https://alitheagenomics.com/rna-preservation-methods-to-improve-rna-quality-and-quantity/): High-quality RNA is essential for high-throughput RNA-seq. It ensures transcriptomic data is accurate, and reliable, and can drive novel findings and conclusions with confidence. Researchers can now choose from many RNA preservation methods to improve RNA quality and quantity for downstream sequencing applications.
- [How do you convert million reads terminology to gigabytes (GB) in NGS?](https://alitheagenomics.com/how-do-you-convert-million-reads-terminology-to-gigabytes-gb-in-next-generation-sequencing/): The data output from next-generation sequencing platforms has undergone explosive growth in recent years thanks to technological advances which have lowered costs (Jiang et al., 2022).
- [How Much RNA is Needed for RNA-seq?](https://alitheagenomics.com/how-much-rna-is-needed-for-rna-seq/): RNA-seq quantifies the genome-wide level of thousands of mRNA transcripts from many samples in a single assay. Researchers can now choose from many next-generation RNA-seq library preparation protocols, and the recommended amount of RNA needed for each of these varies by platform.
- [How does MGI sequencing technology work?](https://alitheagenomics.com/how-does-mgi-sequencing-technology-work/): Advancements in genetic sequencing technology have led to increased accuracy, speed, and cost-effectiveness, which are all factors that are highly valued by customers. As a result, companies are investing heavily in research and development to stay ahead of the competition.
- [How do RNA-seq results compare between Illumina and MGI platforms?](https://alitheagenomics.com/how-do-rna-seq-results-compare-between-illumina-and-mgi-sequencing-platforms/): Illumina has dominated the next-generation sequencing market thanks to its high accuracy and high-throughput sequencing technology. However, MGI Tech, a Beijing Genomics Institute (BGI) Group subsidiary, is now shaking up the sector with its new MGI genetic sequencers. These MGI sequencers offer higher throughput and lower costs, but how do RNA sequencing (RNA-seq) results compare between Illumina and MGI sequencing platforms?
- [Scalability of Illumina and MGI Sequencing Technologies](https://alitheagenomics.com/scalability-of-illumina-and-mgi-sequencing-technologies/): Next-generation sequencing (NGS) has now entered an era of unprecedented scalability. Two companies, Illumina and MGI Tech, lead the way in the ultra-high-throughput chapter of NGS. Illumina and MGI sequencing technologies produce a significant amount of data and allow researchers to simultaneously process more samples at a lower cost than ever before.
- [Illumina TruSeq library prep vs BRB-seq: optimal tradeoff between the number of detected genes and sequencing cost](https://alitheagenomics.com/illumina-truseq-library-prep-versus-mercurius-brb-seq-optimal-tradeoff-between-the-number-of-detected-genes-and-sequencing-cost/): RNA-seq experiments rely on robust library prep stages to generate accurate and reliable transcriptomic data. Different library preparation technologies, such as Illumina TruSeq library prep and MERCURIUS™ BRB-seq, detect similar numbers of expressed genes even at low sequencing depth.
- [How are MERCURIUS™ BRB-seq and DRUG-seq library preps compatible with MGI sequencing?](https://alitheagenomics.com/how-are-mercurius-brb-seq-and-drug-seq-library-preps-compatible-with-mgi-sequencing/): MERCURIUS™ BRB-seq and DRUG-seq library preparations are now compatible with MGI sequencing. This gives researchers maximum flexibility to perform ultra-high-throughput 3’ mRNA-seq experiments where MGI sequencers are available.
- [Shallow Sequencing for Quality Control of Library Preparations](https://alitheagenomics.com/shallow-sequencing-for-quality-control-of-library-preparations/): Shallow sequencing of MERCURIUS™ BRB-seq and MERCURIUS™ DRUG-seq library preparations is a quality control (QC) step to ensure that each multiplexed sample will obtain a uniform number of reads to generate reliable and robust data when the libraries are sequenced deeper.
- [How do our kits for MGI compare to MGIEasy RNA library prep kits?](https://alitheagenomics.com/how-do-mercurius-brb-seq-and-mercurius-drug-seq-library-prep-kits-for-mgi-sequencing-compare-to-mgieasy-rna-library-prep-kits/): MERCURIUS™ BRB-seq and MERCURIUS™ DRUG-seq library preparation kits are compatible with MGI sequencing technology. They provide researchers with a scalable, cost-effective bulk 3’ mRNA-seq solution to ultra-high-throughput transcriptomic experiments where MGI sequencers  are available.
- [What is the LINCS consortium?](https://alitheagenomics.com/what-is-the-lincs-consortium/): The Library of Integrated Network-Based Cellular Signatures (LINCS) consortium from the National Institutes of Health (NIH) is a collective effort to catalog changes in gene expression and other cellular processes that occur when cells undergo genetic or pharmacologic perturbations.
- [What is the L1000 gene expression profiling technology?](https://alitheagenomics.com/what-is-the-l1000-gene-expression-profiling-technology/): L1000 is a high-throughput bead-based gene expression profiling assay that directly measures the mRNA abundance of 978 “landmark” genes selected to represent the diversity of biological pathways and processes in human cells. Researchers use this subset of the transcriptome to computationally infer the expression of an additional 11,350 genes not explicitly measured (Subramanian et al., 2017).
- [What Is RASL-seq and How Can It Contribute to Your Drug Discovery Pipeline?](https://alitheagenomics.com/what-is-rasl-seq-and-how-can-it-contribute-to-your-drug-discovery-pipeline/): In the current ocean of high-throughput sequencing techniques, it can be overwhelming to understand how a particular technology works, what it excels at, and what it struggles to achieve.
- [How RASL-seq Works](https://alitheagenomics.com/how-rasl-seq-works/): RASL-seq is a cost-effective, targeted, high-throughput sequencing technology developed to help researchers, biotechnology, and pharmaceutical companies streamline the discovery of potential therapeutics of tomorrow with genomics (Li et al., 2012; Li, Qiu and Fu, 2012).
- [How Has RASL-seq Contributed to Previous Discoveries?](https://alitheagenomics.com/how-has-rasl-seq-contributed-to-previous-discoveries/): RNA-mediated oligonucleotide Annealing, Selection, and Ligation with Next-Gen sequencing (RASL-seq) is a targeted high-throughput RNA-seq-based technology that has contributed to diverse biological discoveries from the identification of novel cancer therapeutics to the broad importance of alternative splicing in human health and disease.
- [What is TempO-Seq™?](https://alitheagenomics.com/what-is-tempo-seq/): Templated Oligo assay with Sequencing readout (TempO-Seq™) is a ligation-based targeted whole transcriptome expression profiling assay designed to maximize the utilization of precious or limited samples for high-throughput toxicogenomic or drug discovery pipelines (Yeakley et al., 2017).
- [How does MERCURIUS™ DRUG-seq compare to TempO-Seq™ and RASL-seq?](https://alitheagenomics.com/how-does-mercurius-drug-seq-compare-to-tempo-seq-and-rasl-seq/): Determining the transcriptomic effects of novel compounds on cells for large-scale therapeutic or toxicology screens is a critical component of drug development pipelines, allowing researchers to assess the on- or off-target effects of a drug, its toxicity, and possible mechanisms of action.
- [What Are Clariom™ Assays?](https://alitheagenomics.com/what-are-clariom-assays/): Clariom™ assays from Applied Biosystems™ use microarray technology to facilitate broad or targeted transcriptome analysis to identify crucial biomarkers, biological pathways, and complex gene expression signatures suited to diverse user needs.
- [The Clariom™ GO Screen versus MERCURIUS™ DRUG-seq](https://alitheagenomics.com/the-clariom-go-screen-versus-mercurius-drug-seq/): Microarray-based Clariom™ assays from Applied Biosystems™ are a potential option for gene expression profiling studies when looking for a scalable technology to integrate into drug screening pipelines.
- [Affymetrix™ GeneChip™ Microarrays: Where is the technology now?](https://alitheagenomics.com/affymetrix-genechip-microarrays-where-is-the-technology-now/): After almost thirty years since the first commercial prototype of the Affymetrix™ GeneChip™ microarray hit the market in 1994, its impact on our understanding of the intricate role of gene expression in health and disease remains staggering.
- [What Are QuantiGene™ Plex Gene Expression Assays?](https://alitheagenomics.com/what-are-quantigene-plex-gene-expression-assays/): QuantiGene™ Plex Gene Expression Assays from Invitrogen™ use hybridization-probe-based branched DNA technology to simultaneously quantify up to 80 known genes of interest per well of a 96- or 384-well plate.
- [Looking for an RNA-seq method for degraded RNA? Introducing MERCURIUS™ FFPE-seq](https://alitheagenomics.com/looking-for-an-ffpe-rna-seq-method-for-degraded-rna-introducing-mercurius-ffpe-seq/): MERCURIUS™ formalin-fixed paraffin-embedded sequencing (FFPE-seq) is a scalable and cost-effective full-length bulk RNA sequencing technology optimized for heavily degraded RNA samples with RNA integrity numbers (RIN) as low as 1.
- [What is Ion AmpliSeq™ Targeted Sequencing Technology?](https://alitheagenomics.com/what-is-ion-ampliseq-targeted-sequencing-technology/): Ion AmpliSeq™ from Thermo Fisher Scientific is a targeted PCR-based transcriptome profiling technology that allows users to measure the expression levels of over 20,000 genes, even in challenging low-quantity or degraded RNA samples such as from formalin-fixed paraffin-embedded (FFPE) tissue.
- [How Ion AmpliSeq™ Compares to the MERCURIUS™ Family of Technologies](https://alitheagenomics.com/how-ion-ampliseq-compares-to-the-mercurius-family-of-technologies/): A core goal of large-scale drug discovery screens is to use the transcriptomic effects of novel compounds on cells as indicators of both drug toxicity and potential mechanisms of action.
- [When to Use High Sensitivity BRB-seq Over Standard BRB-seq](https://alitheagenomics.com/when-to-use-high-sensitivity-brb-seq-over-standard-brb-seq/): Ultra-low input RNA-seq library preparation methods like our  MERCURIUS™ High Sensitivity BRB-seq kit provide researchers with powerful tools to explore the transcriptomes of small cell populations or precious clinical samples where extracted RNA quantities are minimal. 

## Pages
- [1536 DRUG-seq Webinar Registration](https://alitheagenomics.com/news-and-events/1536webinarregistration/): In this early access launch webinar, Alithea Genomics will introduce MERCURIUS™ 1536 DRUG-seq, a whole transcriptome profiling workflow designed for applications where 384-well transcriptomic screening becomes difficult to scale or where sample material is limited, e.g., with non-proliferating primary cells or iPSCs. By bringing broad transcriptomic readouts into the density and throughput of modern screening, 1536 DRUG-seq enables discovery teams to generate reusable compound-response datasets for primary screening, mechanism-of-action discovery, toxicity detection, compound prioritization, and AI/ML model development. 
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- [News & Events](https://alitheagenomics.com/news-and-events/): Explore our latest news and events
- [BRB-seq](https://alitheagenomics.com/technology/brb-seq/): Unlock the power of unbiased transcriptome profiling with massively multiplexed, ultra-high-content, and high-throughput RNA sequencing.
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## Kits
- [MERCURIUS™ Total Plant BRB-seq Kit](https://alitheagenomics.com/kits/mercurius-total-plant-brb-seq-kit/): MERCURIUS™ Total Plant BRB-seq is a plant total RNA-seq kit for purified plant RNA samples, designed to support scalable whole-transcriptome profiling across plant research, crop science, and agrochemical R&D.
- [MERCURIUS™ 1536 DRUG-seq Kit](https://alitheagenomics.com/kits/mercurius-1536-drug-seq-kit/): MERCURIUS™ 1536 DRUG-seq is an automatable, ultra-high-throughput bulk 3’ mRNA-seq technology designed for frozen 2D cell lines and primary cells in 1536-well assay plates. It enables screening teams to build standardized, foundational compound-response AI training datasets of thousands to millions of transcriptomic profiles, at the scale where 384-well throughput is insufficient.
- [MERCURIUS™ Total Blood BRB-seq Kit](https://alitheagenomics.com/kits/mercurius-total-blood-brb-seq-kits-blood-rna-seq/): MERCURIUS™ Total Blood BRB-seq is a whole blood RNA-seq kit for purified human, rat, or mouse blood RNA samples, combining early multiplexing, inline globin depletion, and full-length total RNA sequencing in one streamlined workflow. The kit generates sequencing-ready libraries for coding and non-coding RNA analysis, while supporting applications such as transcript variant detection, alternative splicing analysis, and fusion gene discovery.
- [Low-input FLASH-seq](https://alitheagenomics.com/kits/mercurius-low-input-flash-seq-kits-ultra-sensitive-and-full-length-library-preparation-kits-for-low-input-rna-samples/): Discover Sample Datasets
- [MERCURIUS™ Total BRB-seq Kit](https://alitheagenomics.com/kits/mercurius-multiplexed-total-rna-seq-kits-full-length-transcriptome-screening/): Built for teams aiming to detect coding and non-coding transcripts, isoforms, and splice variants in purified RNA from larger cohorts, more conditions, or more timepoints than possible with standard total RNA-seq methods.
- [MERCURIUS™ Single-cell FLASH-seq Kit](https://alitheagenomics.com/kits/mercurius-single-cell-flash-seq-kits-extraction-free-library-preparation-kits/): Discover Sample Datasets
- [MERCURIUS™ Spheroid DRUG-seq Kit](https://alitheagenomics.com/kits/mercurius-spheroid-drug-seq-kits-extraction-free-library-preparation-kits/): MERCURIUS™ Spheroid DRUG-seq combines an optimized in-well spheroid lysis buffer with early sample barcoding and multiplexing for sensitive 3’ transcript coverage of coding transcripts in up to 384 samples in a single tube. The scalable, automation-ready one-day workflow is compatible with Illumina® and AVITI™ platforms without compromising depth, data quality, or sensitivity compared to sample-by-sample methods.
- [MERCURIUS™ Total DRUG-seq Kit](https://alitheagenomics.com/kits/mercurius-total-drug-seq-kits-full-length-transcriptome-profiling-for-compound-screening-and-target-validation/): Capture expression, splicing, and isoforms, coding and non-coding RNAs.
- [MERCURIUS™ High-sensitivity BRB-seq Kit](https://alitheagenomics.com/kits/mercurius-high-sensitivity-brb-seq-nr/): Built for teams requiring high-throughput but robust detection of coding transcript expression from diverse species and tissues, even when purified input RNA is scarce. Ideal for studies with larger cohorts, more conditions, or more timepoints than possible to assess with standard high-sensitivity bulk RNA-seq methods.
- [MERCURIUS™ Full-Length BRB-seq Kit](https://alitheagenomics.com/kits/mercurius-full-length-brb-seq-kit/): Discover Sample Datasets
- [MERCURIUS™ BRB-seq Kit](https://alitheagenomics.com/kits/mercurius-brb-seq-kit-bulk-rna-seq-kit/): MERCURIUS™ BRB-seq is a bulk RNA-seq kit for researchers who need cost-effective gene expression profiling across many purified RNA samples. The workflow is designed for academic labs, core facilities, and research teams running studies with larger cohorts, multiple conditions, time points, tissues, species, or perturbations.
- [MERCURIUS™ DRUG-seq Kit](https://alitheagenomics.com/kits/drug-seq-kits/): MERCURIUS™ DRUG-seq is an extraction-free DRUG-seq kit for drug discovery teams that need transcriptome-wide gene expression readouts at a screening scale.

## Publications
- [Haplotype-phased ‘Ottawa 3’ genome unravels differential reaction of apple rootstock roots to mixed viral infection](https://alitheagenomics.com/publication/haplotype-phased-ottawa-3-genome-unravels-differential-reaction-of-apple-rootstock-roots-to-mixed-viral-infection/)
- [Multi‐well plate lid for single‐step pooling of 96 samples for high‐throughput barcode‐based sequencing.](https://alitheagenomics.com/publication/stephanie-boder%e2%80%90pasche-mustafa-demir-sarah-heub-manon-garzuel-real-ischer-daniel-migliozzi-siegfried-graf-noa-schmid-h-baris-atakan/)
- [A stromal cell population that inhibits adipogenesis in mammalian fat depots.](https://alitheagenomics.com/publication/schwalie-p-c-dong-h-zachara-m-russeil-j-alpern-d-akchiche-n-caprara-c-sun-w-schlaudraff-k-u-soldati-g-wolfrum-c-deplancke-b-2018-a-stromal-cell-population-t/)
- [Cell-cycle inhibition preserves robust development but rebalances lineages in mouse gastruloids.](https://alitheagenomics.com/publication/maxine-leonardi-yves-paychere-felix-naef-cell-cycle-inhibition-preserves-robust-development-but-rebalances-lineages-in-mouse-gastruloids/)
- [Spermidine Reproduces the Anti-Inflammatory Effects of Intermittent Fasting and Prevents Urate and Calcium Pyrophosphate Crystal-Induced Inflammation.](https://alitheagenomics.com/publication/pham-c-n-castelli-f-finet-f-leroy-c-chollet-c-chirayath-t-w-moitra-s-zarka-m-ostertag-a-brial-f-combes-c-latourte-a-bardin-t-fenaille-f-richette-p-and-ea-h/)
- [MTCH2 modulates CPT1 activity to regulate lipid metabolism of adipocytes.](https://alitheagenomics.com/publication/wu-c-wang-t-ghosh-a-et-al-mtch2-modulates-cpt1-activity-to-regulate-lipid-metabolism-of-adipocytes/)
- [BioSkel – Towards a Framework for OMICS Applications.](https://alitheagenomics.com/publication/valentin-beauvais-clemence-couton-nicolo-tonci-sebastien-limet-lucile-mollet-thierry-prazuck-and-sophie-robert-bioskel-towards-a-framework-for-omics-applications/)
- [Molecular determinants of brain-resident CD8+ T cell formation and function. ](https://alitheagenomics.com/publication/tarek-elmzzahi-chun-hsi-su-mehrnoush-hadaddzadeh-shakiba-doaa-hamada-daryamalko-maren-koehne-aleksej-frolov-teisha-mason-yuanfang-li-rebekka-scholz-collins-osei-sarpong-leonie-heyden-jonas/)
- [Local niche-derived immunosuppressive CXCR2+ cells impair antiviral immunity.](https://alitheagenomics.com/publication/akisawa-satomi-riho-saito-tadahaya-mizuno-hiroki-sugishita-hideki-ukai-shigeyuki-shichino-masashi-yanagisawa-kouji-matsushima-yukiko-gotoh-to/)
- [Fast and highly sensitive full-length single-cell RNA sequencing using FLASH-seq.](https://alitheagenomics.com/publication/hahaut-v-pavlinic-d-carbone-w-et-al-fast-and-highly-sensitive-full-length-single-cell-rna-sequencing-using-flash-seq/)
- [CRIPTO’s multifaceted role in driving aggressive prostate cancer unveiled by in vivo, organoid, and patient data.](https://alitheagenomics.com/publication/rodrigues-sousa-e-de-brot-s-zoni-e-et-al-criptos-multifaceted-role-in-driving-aggressive-prostate-cancer-unveiled-by-in-vivo-organoid-and-patient-data/)
- [Targeting stemness pathways modulates macrophage polarization and reprograms the tumor microenvironment.](https://alitheagenomics.com/publication/austeja-butkute-marius-baltramonaitis-simona-malmige-adas-darinskas-vita-pasukoniene-agata-mlynska-targeting-stemness-pathways-modulates-macrophage-polarization-and-reprograms-the-tumor-microenv/)
- [In Vitro Evaluation of the Safety and Efficacy of Cibisatamab Using Adult Stem Cell-Derived Organoids and Colorectal Cancer Spheroids.](https://alitheagenomics.com/publication/anstett-v-heinzelmann-e-piraino-f-roch-a-chrisnandy-a-norkin-m-garnier-v-homicsko-k-hoehnel-ka-s-brandenberg-n-in-vitro-evaluation-of-the-safety-and-efficacy-of-cibisatama/)
- [Transcriptional landscape of human keratinocyte models exposed to 60-GHz millimeter-waves.](https://alitheagenomics.com/publication/catherine-martin-bertrand-evrard-frederic-percevault-kate-ryder-thomas-darde-aurelie-lardenois-maxim-zhadobov-ronan-sauleau-frederic-chalmel-yves/)
- [Sustained Vascular Inflammatory Effects of SARS‑CoV‑2 Spike Protein on Human Endothelial Cells.](https://alitheagenomics.com/publication/mitra-gultom-lin-lin-camilla-blunk-brandt-anastasia-milusev-alain-despont-jane-shaw-yvonne-doring-yonglun-luo-robert-rieben-sustained-vascular-inflammatory-effects-of-sars/)
- [Imipridones affect tumor bioenergetics and promote cell lineage differentiation in diffuse midline gliomas.](https://alitheagenomics.com/publication/przystal-j-m-cianciolo-cosentino-c-yadavilli-s-zhang-j-laternser-s-bonner-e-r-prasad-r-dawood-a-a-lobeto-n-chin-chong-w-biery-m-c-myers-c-olson-j-m-panditha/)
- [Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells.](https://alitheagenomics.com/publication/mouri-k-guo-m-h-de-boer-c-g-lissner-m-m-harten-i-a-newby-g-a-deberg-h-a-platt-w-f-gentili-m-liu-d-r-campbell-d-j-hacohen-n-tewhey-r-ray-j-p-202/)
- [Time-resolved characterization of the innate immune response in the respiratory epithelium of human, porcine, and bovine during influenza virus infection.](https://alitheagenomics.com/publication/laloli-l-licheri-m-f-probst-l-licheri-m-gultom-m-holwerda-m-vkovski-p-dijkman-r-2022-time-resolved-characterization-of-the-innate-immune-response-in-the-respira/)
- [Katarina Pinjusic, Giovanna Ambrosini, Joao Lourenco, Nadine Fournier, Christian Iseli, Nicolas Guex, Olga Egorova, Sina Nassiri and Daniel B. Constam. Inhibition of anti-tumor immunity by melanoma cell-derived Activin-A depends on STING.](https://alitheagenomics.com/publication/katarina-pinjusic-giovanna-ambrosini-joao-lourenco-nadine-fournier-christian-iseli-nicolas-guex-olga-egorova-sina-nassiri-and-daniel-b-constam-inhibition-of-anti-tumor-immunity-by-melanoma-ce/)
- [Radiana Ferrero, Pernille Yde Rainer, Marie Rumpler, Julie Russeil, Magda Zachara, Joern Pezoldt, Guido van Mierlo, Vincent Gardeux, Wouter Saelens, Daniel Alpern, Lucie Favre, Nathalie Vionnet, Styliani Mantziari, Tobias Zingg, Nelly Pitteloud, Michel Suter, Maurice Matter, Kai-Uwe Schlaudraff, Carles Canto, and Bart Deplancke. A human omentum-specific mesothelial-like stromal population inhibits adipogenesis through IGFBP2 secretion.](https://alitheagenomics.com/publication/radiana-ferrero-pernille-yde-rainer-marie-rumpler-julie-russeil-magda-zachara-joern-pezoldt-guido-van-mierlo-vincent-gardeux-wouter-saelens-daniel-2/)
- [Radiana Ferrero, Pernille Yde Rainer, Marie Rumpler, Julie Russeil, Magda Zachara, Joern Pezoldt, Guido van Mierlo, Vincent Gardeux, Wouter Saelens, Daniel Alpern, Lucie Favre, Nathalie Vionnet, Styliani Mantziari, Tobias Zingg, Nelly Pitteloud, Michel Suter, Maurice Matter, Kai-Uwe Schlaudraff, Carles Canto, and Bart Deplancke. A human omentum-specific mesothelial-like stromal population inhibits adipogenesis through IGFBP2 secretion.](https://alitheagenomics.com/publication/radiana-ferrero-pernille-yde-rainer-marie-rumpler-julie-russeil-magda-zachara-joern-pezoldt-guido-van-mierlo-vincent-gardeux-wouter-saelens-daniel/)
- [Transcriptomic profiling of the response to excess iodide in Keap1 hypomorphic mice reveals new gene-environment interactions in thyroid homeostasis.](https://alitheagenomics.com/publication/panos-g-ziros-dionysios-v-chartoumpekis-ilias-georgakopoulos-soares-georgios-psarias-gerasimos-p-sykiotis-transcriptomic-profiling-of-the-response-to-excess-iodide-in-keap1-hypomorphic-mice-re/)
- [Multiscale physiological responses to nitrogen supplementation of maize hybrids.](https://alitheagenomics.com/publication/sheng-ying-brandon-webster-lina-gomez-cano-kiran-kumar-shivaiah-qianjie-wang-linsey-newton-erich-grotewold-addie-thompson-and-peter-k-lundquist-multiscale-physiological-responses-to-nitrogen/)
- [CRISPR‑Cas9 genetic screen leads to the discovery of L‑Moses, a KAT2B inhibitor that attenuates Tunicamycin‑mediated neuronal cell death.](https://alitheagenomics.com/publication/sofa-pavlou-stefanie-foskolou-nikolaos-patikas-sarah-f-field-evangelia-k-papachristou-clive-d-santos-abigail-r-edwards-kamal-kishore-rizwan-ansari-sandeep-s-rajan-hugo-j-r-fer/)
- [Measuring transcription factor binding and gene expression using barcoded self-reporting transposon calling cards and transcriptomes.](https://alitheagenomics.com/publication/lalli-m-yen-a-thopte-u-dong-f-moudgil-a-chen-x-milbrandt-j-dougherty-joseph-d-mitra-robi-d-2022-measuring-transcription-factor-binding-and-gene-expression-us/)
- [Genetic variation near CXCL12 is associated with susceptibility to HIV-related non-Hodgkin lymphoma.](https://alitheagenomics.com/publication/christian-w-t-tiphaine-o-m-nava-e-christian-h-federico-a-s-jonathan-n-dominique-c-cecile-g-laurence-m-sophia-s-w-shehnaz-k-h-ioannis-t-matthias-c-andri-r/)
- [Extensive tissue-specific expression variation and novel regulators underlying circadian behavior.](https://alitheagenomics.com/publication/litovchenko-m-meireles-filho-a-c-a-frochaux-m-v-bevers-r-p-j-prunotto-a-anduaga-a-m-hollis-b-gardeux-v-braman-v-s-russeil-j-m-c-kadener-s-dal-peraro-m-amp/)
- [Systems-Genetics-Based Inference of a Core Regulatory Network Underlying White Fat Browning.](https://alitheagenomics.com/publication/li-y-schwalie-p-c-bast-habersbrunner-a-mocek-s-russeil-j-fromme-t-deplancke-b-klingenspor-m-2019-systems-genetics-based-inference-of-a-core-regulatory-network-underlying/)
- [Unusual nucleosome formation and transcriptome influence by the histone H3mm18 variant.](https://alitheagenomics.com/publication/hirai-s-tomimatsu-k-miyawaki-kuwakado-a-takizawa-y-komatsu-t-tachibana-t-fukushima-y-takeda-y-negishi-l-kujirai-t-koyama-m-ohkawa-y-kurumizaka-h-2021-unusu/)
- [Profiling the Atopic Dermatitis Epidermal Transcriptome by Tape Stripping and BRB-seq.](https://alitheagenomics.com/publication/hu-t-todberg-t-andersen-d-danneskiold-samsoe-n-b-hansen-s-b-n-kristiansen-k-ewald-d-a-brix-s-rosa-j-c-d-hoof-i-skov-l-litman-t-2022-profiling-the-atopic/)
- [Mitochondrial gene signature in the prefrontal cortex for differential susceptibility to chronic stress.](https://alitheagenomics.com/publication/weger-m-alpern-d-cherix-a-ghosal-s-grosse-j-russeil-j-gruetter-r-de-kloet-e-r-deplancke-b-sandi-c-2020-mitochondrial-gene-signature-in-the-prefrontal-cortex-for-di/)
- [The Hippo pathway controls myofibril assembly and muscle fiber growth by regulating sarcomeric gene expression.](https://alitheagenomics.com/publication/kaya-copur-a-marchiano-f-hein-m-y-alpern-d-russeil-j-luis-n-m-mann-m-deplancke-b-habermann-b-h-schnorrer-f-2021-the-hippo-pathway-controls-myofibril-assembly-and/)
- [Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo.](https://alitheagenomics.com/publication/liu-j-frochaux-m-gardeux-v-deplancke-b-robinson-rechavi-m-2020-inter-embryo-gene-expression-variability-recapitulates-the-hourglass-pattern-of-evo-devo/)
- [Commensal Gut Bacteria Buffer the Impact of Host Genetic Variants on Drosophila Developmental Traits under Nutritional Stress.](https://alitheagenomics.com/publication/ma-d-bou-sleiman-m-joncour-p-indelicato-c-e-frochaux-m-braman-v-litovchenko-m-storelli-g-deplancke-b-leulier-f-2019-commensal-gut-bacteria-buffer-the-impact-of-hos/)
- [Sex-dependent and sex-independent regulatory systems of size variation in natural populations.](https://alitheagenomics.com/publication/okada-h-yagi-r-gardeux-v-deplancke-b-hafen-e-2019-sex-dependent-and-sex-independent-regulatory-systems-of-size-variation-in-natural-populations/)
- [LncRNA Ctcflos orchestrates transcription and alternative splicing in thermogenic adipogenesis.](https://alitheagenomics.com/publication/bast-habersbrunner-a-kiefer-c-weber-p-fromme-t-schiesl-a-schwalie-p-c-deplancke-b-li-y-klingenspor-m-2021-lncrna-ctcflos-orchestrates-transcription-and-alternative-sp/)
- [Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel.](https://alitheagenomics.com/publication/bevers-r-p-j-litovchenko-m-kapopoulou-a-braman-v-s-robinson-m-r-auwerx-j-hollis-b-deplancke-b-2019-mitochondrial-haplotypes-affect-metabolic-phenotypes-in-the-drosoph/)
- [Cooperative Blockade of CK2 and ATM Kinases Drives Apoptosis in VHL-Deficient Renal Carcinoma Cells through ROS Overproduction.](https://alitheagenomics.com/publication/giacosa-s-pillet-c-seraudie-i-guyon-l-wallez-y-roelants-c-battail-c-evrard-b-chalmel-f-barette-c-soleilhac-e-fauvarque-m-o-franquet-q-sarrazin-c-peilleron-n/)
- [Cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel.](https://alitheagenomics.com/publication/frochaux-m-v-bou-sleiman-m-gardeux-v-dainese-r-hollis-b-litovchenko-m-braman-v-s-andreani-t-osman-d-deplancke-b-2020-cis-regulatory-variation-modulates-susceptibi/)
- [Distinct Gene Set Enrichment Profiles in Eosinophilic and Non-Eosinophilic Chronic Rhinosinusitis with Nasal Polyps by Bulk RNA Barcoding and Sequencing.](https://alitheagenomics.com/publication/ishino-t-takeno-s-takemoto-k-yamato-k-oda-t-nishida-m-horibe-y-chikuie-n-kono-t-taruya-t-hamamoto-t-ueda-t-2022-distinct-gene-set-enrichment-profiles-in-eosin/)
- [Classification of four distinct osteoarthritis subtypes with a knee joint tissue transcriptome atlas.](https://alitheagenomics.com/publication/yuan-c-pan-z-zhao-k-li-j-sheng-z-yao-x-liu-h-zhang-x-yang-y-yu-d-zhang-y-xu-y-zhang-z-y-huang-t-liu-w-ouyang-h-2020-classification-of-four-distin/)

## Services
- [Total Plant BRB-seq Service](https://alitheagenomics.com/services/total-plant-brb-seq/): Streamlined total RNA-seq service for purified plant RNA, combining plant-focused rRNA depletion with early multiplexing to make whole-transcriptome profiling more accessible across plant research, crop science, and agrochemical R&D.
- [Total Blood BRB-seq](https://alitheagenomics.com/services/total-blood-brb-seq-whole-blood-rna-seq-service/): Total Blood BRB-seq enables industrial and academic clients to generate scalable total RNA-seq data directly from whole blood with integrated globin depletion for maximum detection of coding and non-coding transcripts
- [Total BRB-seq](https://alitheagenomics.com/services/multiplexed-total-rna-seq-services-rna-seq-service-alithea-genomics/): Full-length and total RNA-seq combined with massive sample multiplexing.
- [Low-input FLASH-seq](https://alitheagenomics.com/services/low-input-flash-seq-service-ultra-sensitive-and-full-length-low-input-rna-seq-service-alithea-genomics/): This service enables full-length mRNA transcript coverage from low RNA inputs from precious samples (1pg to 1ng).
- [Spheroid DRUG-seq](https://alitheagenomics.com/services/organoid-drug-seq/): Our Spheroid DRUG-seq service provides industry and academic scientists with ultra-scalable RNA-seq optimized for 3D cellular models, enabling highly sensitive, RNA-extraction-free, and extremely cost-effective transcriptomic screens for large-scale compound discovery programs, next-generation toxicology strategies, and mechanism-of-action studies.
- [High-sensitivity BRB-seq ](https://alitheagenomics.com/services/high-sensitivity-low-input-brb-seq/): Massively multiplexed low-input RNA-seq, compatible with low-input RNA samples from 1ng.
- [Full-length BRB-seq](https://alitheagenomics.com/services/multiplexed-rna-seq-mrna-service/): Full-length mRNA-seq combined with massive sample multiplexing.
- [BRB-seq](https://alitheagenomics.com/services/brb-seq/): Our BRB-seq service enables industrial and academic scientists to outsource unbiased gene expression profiling at scale, with no trade-off in data quality compared to standard methods.
- [Single-cell FLASH-seq](https://alitheagenomics.com/services/single-cell-flash-seq-service-ultra-sensitive-and-full-length-single-cell-sequencing/): This service provides full-length mRNA transcript coverage even for low-abundance genes, empowering researchers to explore differential gene expression, detect alternative splicing, and analyze isoform diversity without RNA extraction.
- [Total DRUG-seq](https://alitheagenomics.com/services/total-drug-seq-services-rna-seq-service-alithea-genomics/): Our Total DRUG-seq service provides industry and academic scientists with ultra-scalable total RNA-seq, enabling whole-transcriptome screens of full-length coding and non-coding transcripts when isoform and alternative splicing detection is crucial. Ideal for large-scale compound discovery programs, next-generation toxicology strategies, and mechanism-of-action studies.
- [DRUG-seq](https://alitheagenomics.com/services/drug-seq/): Our DRUG-seq service provides industry and academic scientists with ultra-scalable RNA-seq that enables highly sensitive, RNA-extraction-free, massively multiplexed, and extremely cost-effective transcriptomic screens for large-scale compound discovery programs, next-generation toxicology strategies, and mechanism-of-action studies.