RNA sequencing services, compared per sample and per read

Advertised prices, verified

What sets an RNA-seq price

1. Library preparation chemistry. Poly-A selection is the standard and cheapest choice for intact eukaryotic mRNA. Ribosomal depletion costs more and is required for degraded samples, bacterial RNA and any work where non-polyadenylated transcripts matter. The chemistry is chosen by your sample, not by your budget, and it changes the per-sample price before depth is considered.
2. Depth, in reads per sample. Depth is the main dial on cost. Standard differential expression on a well-annotated genome needs far fewer reads than isoform-level work or low-expression transcript discovery, and paying for depth an experiment cannot use is the most common way an RNA-seq budget is wasted.
3. Read length and pairing. Single-end short reads are adequate for counting transcripts against a reference. Paired-end and longer reads cost more and earn it only where isoforms, fusions or novel transcripts are the point of the experiment. Match this to the question, not to the best specification offered.
4. Analysis: included, extra, or yours. Some quotes stop at demultiplexed FASTQ files, others include alignment, counts and a differential expression report. That difference is easily the largest uncontrolled variable between two per-sample prices, and it is the first thing to normalise when comparing.

Sample quality decides more than vendor choice

RNA integrity is the input that determines whether the experiment works at all. Vendors will run an integrity check on receipt and will tell you when a sample is marginal, but by then the sample has been collected and the collection cannot usually be repeated. Handling at the bench matters more to the result than the difference between two competent providers.

Ask what a vendor does when a sample fails incoming QC: whether it is dropped from the batch, re-prepped at cost, or proceeds with a note. That policy is a real cost difference on any project where some samples are precious or marginal.

Replicates before depth, almost always

For differential expression, adding biological replicates buys more statistical power than adding reads to the same libraries, and the cost per replicate at moderate depth is often lower than the cost of doubling depth. A quote that maximises reads per sample within a fixed budget is frequently the wrong shape for the experiment.

Decide the design first, then buy the depth the design needs. Vendors will happily quote either way, and the cheaper quote is not necessarily the one that answers your question.

Common questions

How much does RNA sequencing cost per sample?

It depends on library chemistry, depth and whether analysis is included. The vendors in this index that publish a per-sample figure are shown above, quoted verbatim with the date; treat a published per-sample price as an entry point and confirm what depth and analysis it assumes.

How many reads do I need?

Standard differential expression against a well-annotated reference needs far fewer reads than isoform-level or discovery work. Set depth from the question you are answering, and put spare budget into biological replicates before extra reads.

Poly-A selection or ribosomal depletion?

Poly-A for intact eukaryotic mRNA, which is most experiments and is cheaper. Ribosomal depletion for degraded RNA, bacterial samples, and any work where non-polyadenylated transcripts are part of the question.

Is analysis included in the price?

Sometimes, and it is the biggest hidden difference between quotes. Ask whether the price ends at FASTQ files or includes alignment, counts and a differential expression report, and normalise for that before comparing per-sample figures.

Browse by service class

• Compare Gene synthesis on advertised prices