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.
This article breaks down the types of RNA-seq services we offer, outlines the sample requirements, and addresses the questions we receive most frequently.
Our RNA-Seq Service: Made for High-Throughput Screening
We specialize in massively multiplexed RNA-seq technologies that enable cost-effective high-throughput screening for different needs.
For instance, we regularly assist clients in the pharmaceutical, biotechnology, agritech, cosmetics, and AI sectors to generate large-scale, unbiased transcriptome-wide gene expression data for various types of screening pipelines.
These screens often include toxicology and mechanism-of-action studies, target identification and hit-to-lead screening, or the rapid generation of training data for artificial intelligence (AI) models.
Meet our MERCURIUS™ RNA-seq Technologies
Our MERCURIUS™ family of technologies offers two primary options, depending on whether your input sample type is cell lysates or purified RNA.
- For cell lysates, we recommend our MERCURIUS™ DRUG-seq service for bulk RNA and our MERCURIUS™ FLASH-seq service for FACS-sorted single cells.
Both technologies are completely RNA-extraction-free and work directly on the washed and frozen cells you send us. For large-scale compound or genetic perturbation screens, this removes tedious, costly, and time-consuming preliminary RNA preparation phases. Just treat and send. - If you have purified RNA, our MERCURIUS™ BRB-seq service is more suitable.
We’ve optimized this technology for RNA that you have already purified in-house. It provides robust results for even small quantities of degraded RNA.
RNA-Seq Services for Every Need
We offer different types of MERCURIUS™ DRUG-seq and MERCURIUS™ BRB-seq services suited to different research hypotheses, budgets, and experimental setups. Both are bulk RNA-seq approaches. In contrast, MERCURIUS™ FLASH-seq is designed for single-cell studies.
Our services are listed in the tables below, along with some example uses (Tables 1 and 2).
If you already know which service you need, skip ahead to the sample requirements section.
|
Starting Material |
Service |
Technology |
Use Case |
|
Cell lysates
|
DRUG-seq |
3’ mRNA-seq |
Unbiased transcriptome-wide gene expression detection and differential expression |
|
Full-length DRUG-seq (early access) |
Full-length mRNA-seq |
Unbiased transcriptome-wide detection of whole transcripts, isoforms, alternative splicing events, and differential expression |
|
|
Targeted DRUG-seq |
Custom gene detection panels |
Targeted expression detection of up to 100 genes |
|
|
FLASH-seq |
Full-length single-cell mRNA-seq |
Unbiased transcriptome-wide detection of whole transcripts, isoforms, alternative splicing events, and differential expression in single cells |
Table 1. Overview of the MERCURIUS™ DRUG-seq and MERCURIUS™ FLASH-seq services suitable for cell lysates
|
Starting Material |
Service |
Technology |
Use Case |
|
Purified RNA
|
BRB-seq |
3’ mRNA-seq |
Unbiased transcriptome-wide gene expression detection and differential expression |
|
High-sensitivity BRB-seq |
3’ mRNA-seq |
Unbiased transcriptome-wide gene expression detection and differential expression from as low as 100 pg RNA per sample |
|
|
Blood BRB-seq |
3’ mRNA-seq |
Transcriptome-wide gene expression detection and differential expression from whole blood with integrated globin depletion |
|
|
Plant BRB-seq |
3’ mRNA-seq |
Unbiased transcriptome-wide gene expression detection and differential expression dedicated to plant RNA. |
|
|
Targeted BRB-seq |
Custom gene detection panels |
Targeted expression detection of up to 100 genes |
|
|
Multiplexed mRNA-seq |
Full-length mRNA-seq |
Unbiased transcriptome-wide detection of whole transcripts, isoforms, alternative splicing events, and differential expression |
|
|
FFPE-seq |
Full-length Total RNA-seq |
Unbiased transcriptome-wide detection of whole transcripts, isoforms, alternative splicing events, and differential expression in RNA with RIN as low as 1 |
Table 2. Overview of the MERCURIUS™ BRB-seq services suitable for purified RNA
Sample Requirements for Each RNA-seq Service
Each of our technologies has different recommended sample requirements, such as the number of cells per well, RNA concentrations, or RNA qualities (Tables 3 and 4).
For more information, you can check our submission guidelines for each service on its dedicated service page.
Starting Material - Cell lysates
|
Service |
Recommended Input |
Preparation Info |
|
DRUG-seq |
96-well plate: 15,000-50,000 cells per well 384-well plate: 2,000-10,000 cells per well
|
Seed only one type of cell per well. Use only one cell type per pool. Ensure a minimum of 80,000 cells per pool. Wash cells with DPBS and store in the original culturing plates at -80°C until shipment. |
|
Full-Length DRUG-seq (early access) |
96-well plate: 5,000-25,000 cells per well 384-well plate: 2,000-10,000 cells per well N.B. The number of cells per well must be uniform to ensure an even distribution of reads after sequencing |
Seed only one type of cell per well. Use only one cell type per pool. Ensure a minimum of 80,000 cells per pool. Wash cells with DPBS and store in the original culturing plates at -80°C until shipment.
|
|
Targeted DRUG-seq |
96-well plate: 15,000-50,000 cells per well |
First, complete and send the gene panel submission form. Wash cells with DPBS, lyse with the provided cell lysis buffer, and transfer to the provided 96-well PCR plate. Store at -80oC until shipment. |
|
FLASH-seq |
96-well plate: 96 FACS-sorted cells 384-well plate: 384 FACS-sorted cells |
Users should directly FACS-sort a single cell to the center of each well of the dedicated plate containing lysis buffer. |
Table 3. Overview of sample requirements and preparation recommendations for the MERCURIUS™ DRUG-seq and MERCURIUS™ FLASH-seq services
Starting Material - Purified RNA
|
Service |
Recommended Input |
Preparation Info |
|
BRB-seq |
96-well and 384-well plate: 200 – 1000 ng total RNA per well in a min. vol. of 15 μL. Concentration >12 ng/μL RIN > 6 260/230 ratio between 1.8 and 2.2 N.B. The RNA amount, integrity, and 260/230 ratios must be uniform across all samples to ensure an even distribution of reads after sequencing |
Extract RNA from all samples in a single batch to limit technical variation. For differential expression, include respective RNA samples in the same library to avoid biases. Pipette RNA samples into the provided 96-well or 384-well PCR plate according to the sample submission form. |
|
High-sensitivity BRB-seq |
96-well and 384-well plate: 100 pg – 500 ng total RNA per well in a min. vol. of 15 μL. Concentration > 2 ng/μL RIN > 6 260/230 ratio between 1.8 and 2.2 N.B. The RNA amount, integrity, and 260/230 ratios must be uniform across all samples to ensure an even distribution of reads after sequencing |
Extract RNA from all samples in a single batch to limit technical variation. For differential expression, include respective RNA samples in the same library to avoid biases. Pipette RNA samples into the provided 96-well or 384-well PCR plate according to the sample submission form.
|
|
Blood BRB-seq |
Send whole blood samples collected in PAXgene or Tempus Blood RNA and RNA Shield tubes. We’ll perform the RNA extraction directly. |
Send us your samples in PAXgene or Tempus Blood RNA and RNA Shield tubes. We’ll do the rest. |
|
Targeted BRB-seq |
96- and 384-well plates: 200–1000 ng total RNA per well in a minimum volume of 20 μL. RIN > 6 260/230 ratio > 1.5 N.B. The RNA amount, integrity, and 260/230 ratios must be uniform across all samples to ensure an even distribution of reads after sequencing |
First, complete and submit the gene panel submission form along with the test samples. Wash cells with DPBS, lyse with the provided cell lysis buffer, and transfer to the provided 96-well PCR plate as per the sample submission form. Store at -80oC until shipment.
|
|
Multiplexed mRNA-seq (early access) |
96-well plate: 500 ng total RNA per well in 20 μL volume. RIN > 7 260/230 ratio between 1.8 and 2.2 N.B. The RNA amount, integrity, and 260/230 ratios must be uniform across all samples to ensure an even distribution of reads after sequencing |
Extract RNA from all samples in a single batch to limit technical variation. For differential expression, include respective RNA samples in the same library to avoid biases. Pipette RNA samples into the provided 96-well PCR plate according to the sample submission form. |
|
FFPE-seq |
96- and 384-well plates: 100–1000 ng total RNA per well in a minimum volume of 10 μL. Accepted RIN 1-10, but ensure all samples have a similar RIN range (i.e., 2 - 7 or >7) 260/230 ratio between 1.8 and 2.2. N.B. The RNA amount, integrity, and 260/230 ratios must be uniform across all samples to ensure an even distribution of reads after sequencing |
Extract RNA from all samples in a single batch to limit technical variation. For differential expression, include respective RNA samples in the same library to avoid biases. Pipette RNA samples into the provided 96-well PCR plate according to the sample submission form. |
Table 4. Overview of sample requirements and preparation recommendations for the MERCURIUS™ BRB-seq services
What’s included in the RNA-seq service?
At Alithea, we’re not a one-size-fits-all service provider. We offer bespoke RNA-seq services tailored to your specific needs. We understand that the objectives, experimental design, and sample types of each screen are unique to your study, and we collaborate with you to achieve the best possible outcome. So, if you’ve 96 samples or 50,000, rest assured that they’re in safe hands.
Feel free to contact us for a complimentary exploratory call to determine if our technology and service are a good fit for you.
Our typical service includes MERCURIUS™ library preparation, quality control, next-generation sequencing, and data analysis. However, sometimes you might need a little more help to achieve your screening goals. That’s why we now also offer comprehensive end-to-end screening services, including cell culture and treatment, Cell Painting, library preparation with any of our MERCURIUS™ technologies, and downstream analysis. Simply discuss your requirements with us, and we'll take care of the rest.
We always include rigorous quality control steps in all our pipelines to ensure you can trust your results and make rapid, confident decisions post-screen. If there’s anything wrong or unclear with samples, we’ll contact you to keep you informed every step of the way.
Here’s what’s usually included in our standard MERCURIUS™ DRUG-seq service pipeline after we receive your frozen 96- or 384-well plates containing cell lysate:
- Library preparation
- Library QC (Qbit, Fragment analyzer, shallow sequencing) - Client checkpoint
- Deep sequencing
- Data preprocessing and reporting - Client checkpoint
- Optional: Data analysis
MERCURIUS™ FLASH-seq service has a similar workflow.
For the purified RNA samples, our standard MERCURIUS™ BRB-seq service pipeline begins with:
- Incoming QC (nano drop and Fragment analyzer) - Client checkpoint
- Library preparation
- Library QC (Qbit, Fragment analyzer, shallow sequencing) - Client checkpoint
- Deep sequencing
- Data preprocessing and reporting - Client checkpoint
- Optional: Data analysis
What’s the turnaround time?
We take pride in our ability to deliver rapid project turnaround times. We’re one of the fastest RNA-seq service providers on the market, particularly for large-scale screening studies involving hundreds or thousands of samples.
For MERCURIUS™ DRUG-seq protocols, we aim for a turnaround of approximately two weeks from the point we receive your cell lysate plates.
For MERCURIUS™ BRB-seq workflows, the additional QC step before library preparation results in an average turnaround time of approximately three weeks from total RNA samples to data.
For Targeted DRUG-seq and Targeted BRB-seq, we need between four and eight weeks to develop and validate your custom gene detection panels on your preliminary samples. Due to this optimization phase, our targeted workflows typically take a maximum of three months in total.
For MERCURIUS™ FLASH-seq library preparation, the process typically takes around four weeks from the time we receive your samples.
What data analysis services are included?
Your data is only as good as the analyses you perform with it.
As part of our standard service pipeline, we demultiplex and align the generated data to the chosen genome, provide a detailed report on the alignment and gene counting statistics, and deliver ready-to-use gene count matrices for downstream analysis.
For researchers requiring more in-depth analysis, our bioinformatics team can generate publication-quality figures tailored to your specific requirements, whether that involves large-scale differential expression, pathway enrichment assessment, or compound correlations for deeper biological insights.
Interested in our RNA-seq service? Next Steps.
The strategic decision to partner with a reliable RNA-seq service provider specialized in transcriptomic screening is a powerful accelerator for pharma, biotech, agritech, cosmetics, and AI model developers aiming to make crucial go/no-go decisions on the future of discovery and development pipelines.
So, if you’re interested in scaling your transcriptomic screens and maximizing your budget without overextending your team or investing in expensive in-house next-generation sequencing infrastructure, contact us for a complimentary exploratory call to discuss your requirements, whether you have 96 samples or 50,000.
