Considering using an RNA-seq service? Read this first…
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.
However, it's crucial that you choose a partner who understands your needs, communicates proactively, and delivers robust data that addresses your hypotheses. Reliable RNA-seq service providers can make the difference between a stalled project and a breakthrough in target discovery and validation, mechanism-of-action studies, or toxicogenomic screens.
So, whether you lack the workforce, the NGS instruments, or have thousands of samples, tight budgets, and no time for troubleshooting, here’s how to select the right RNA-seq service provider and avoid data quality issues, long delays, and surprise costs.
Download our free RNA-seq Service Provider Checklist for 10 questions to ask before you commit. It’ll help you avoid any expensive mistakes down the line!
What Screening-Focused Teams Should Look for in an RNA-seq Service
Not all gene expression profiling approaches are equally suited to screening hundreds or thousands of samples, so it’s essential that any RNA-seq service partner you’re considering is specialized in the most appropriate and scalable method possible and can provide robust data that directly answers your hypotheses. For instance, do you need unbiased bulk or single-cell RNA-seq, or are targeted approaches more suitable? How many and what type of samples will you have?
Here are some essential things to keep in mind when finding a provider who understands your experimental context and is aligned with your goals:
1. The type of RNA-seq service the provider specializes in, and the compatibility with your sample type
Are they bulk or scRNA-seq experts? Specialists in targeted panels or ultra-scalable, unbiased RNA-seq technologies? Select vendors with extensive experience in the most appropriate RNA-seq technology for your question and chosen sample type.
Consider if they support RNA-seq for cell lysates, low-input samples, primary cells, blood, FFPE-derived RNA, or fragile organoid models. Some services might accept degraded RNA, whereas others might not. Do you need to extract RNA first, or is the technology RNA-extraction-free like MERCURIUS™ DRUG-seq? Failure to understand the available options (and their limitations) could lead to suboptimal results in the long run.
2. Their capacity for large-scale or high-throughput projects
Can they process hundreds or thousands of conditions in parallel using unbiased, plate-based multiplex barcoding strategies like DRUG-seq, BRB-seq, or similar? This scalability dramatically lowers your cost per sample, which is essential in screening vast compound or genetic perturbation libraries. Otherwise, costs can spiral.
Traditional approaches, like TaqMan™ gene expression assays or Illumina TruSeq library preps, fall short in terms of information content or struggle with large sample sizes. Other, more scalable gene expression profiling options, like TempO-seq™, suffer biases as they rely on prior probe-based target selection, so they miss novel transcripts or isoforms that could highlight mechanisms of action or off-target effects. The level of scalability and information content required depends on your study design.
Need a quick way to compare RNA-seq service providers? Download our free 10-question checklist to help you evaluate providers before committing.
3. The turnaround time
Screening is time-sensitive. If your RNA-seq service provider takes months to send your data, you risk missing decision points for follow-up experiments, investor updates, or project milestones.
Ask upfront for timelines for library prep, sequencing, and data delivery, especially for large batches. This way, you’ll avoid costly delays and be able to plan your screens accordingly.
4. The extent of services provided
Some service providers, like Alithea Genomics, can act as contract research organizations, offering bespoke comprehensive screening workflows that incorporate high-throughput transcriptomics and high-content screens utilizing technologies like MERCURIUS™ DRUG-seq and Cell Painting. This powerful combination of multimodal
screening data would require extensive expertise and capital expenditure to achieve in-house. Alithea Genomics offers this combined service.
In contrast, some vendors exclusively focus on RNA-seq and perform the entire pipeline, from RNA extraction and library preparation to sequencing and bioinformatics analysis. Others require you to send pre-made libraries or analyze the data yourself. It’s essential to know what to expect to avoid any surprises.
Final Thoughts on Selecting an RNA-seq Service
For biotech and pharma companies, high-throughput RNA-seq screens can help fast-track critical decisions from target validation to candidate selection and many aspects of your pipeline in between. The right service partner can make all the difference.
Now you know what to look for, you can align your choice of provider with your study design and goals. You can scale your transcriptomic screens without overextending your team or investing in expensive in-house next-generation sequencing infrastructure, while eliminating bottlenecks and generating the data you need faster.
Don’t forget to access our free RNA-seq Service Provider Checklist for 10 questions you should ask when searching for a transcriptomic screening vendor. It's the first step toward better collaborations, faster progress, and fewer surprises.
Want to learn more about the high-throughput transcriptomic screening options we offer? Contact us for a free consultation and accelerate your pipeline today.
