Bulk RNA sequencing

Cost-effective bulk RNA sequencing

Use our highly cost-effective low-input bulk RNA sequencing service to generate transcriptome data at population level.

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HomeTechnologyBulk RNA sequencing

Detect transcriptome profiles in populations

Bulk RNA-sequencing is the method of choice for transcriptomics analysis of pooled cell populations, tissue sections or biopsies.

This method has been instrumental in the development of many single-cell RNA sequencing methods.

At Single Cell Discoveries, we offer cost-effective bulk RNA sequencing with sample barcoding and multiplexing.

We use the same CEL-seq2 style barcodes as for our SORT-seq technology to enable multiplexing of samples.

Each sample gets its own sample-specific barcode, which allows us to pool multiple samples into one sequencing library.

This multiplexing approach reduces processing costs significantly, allowing us to offer our bulk RNA sequencing services at highly competitive rates.

Furthermore, the use of single-cell sequencing reagents allows us to process bulk samples with as few as 100 cells as input.

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Key benefits of bulk RNA sequencing

  • Directly comparable with SORT-seq data
    Our bulk RNA sequencing service is based on the same chemistry as our SORT-seq technology for single-cell sequencing. This means that you can directly compare results from your single-cell sequencing experiments with the results from your bulk RNA analysis.
  • Start with just 100 cells
    Because we use single-cell reagents, we can perform a bulk RNA sequencing analysis on extremely low sample volumes. We only need 100 cells for bulk RNA sequencing.
  • Highly competitive pricing 
    Our ability to multiplex samples means our prices are usually much lower than those of other commercial service providers.

How it works

Step 1: RNA purification

The protocol begins with RNA purification. Send us readily isolated RNA, or sort your cells in TRIzol before sending them to us. We perform RNA purification in our lab for cells sorted in TRIzol.

RNA purification of Bulk RNA seq
Sample processing of bulk RNA seq

Step 2: Sample processing

In the lab, we'll use an adapted version of the CEL-seq2 protocol to barcode your sample individually. After barcoding, we'll multiplex all your samples into one sequencing library.

Step 3: Sequencing and data analysis

Next, we'll send the library out for sequencing by one of our sequencing partners. Once we've received that raw data, we'll map it to the appropriate reference transcriptome. Finally, we'll send you the mapped count tables and quality control plots.

Data analysis


As with all of our services, we provide ongoing support from our sequencing specialists. For each bulk RNA sequencing project, we provide the following:

  • Regular email updates during sample processing
  • Raw sequencing data (FASTQ files)
  • A QC report
  • Mapped count tables for downstream analysis

Once we have sent you the data, we'll invite you to schedule a call with one of our scientists to go over any additional questions you may have.

That's when we can discuss any additional data analysis you may need.


How deep should I sequence my samples?

This depends on the number of samples you have, your budget, and your biological question.

Typically, we offer two different packages for bulk RNA sequencing: STANDARD with 10 million sequencing reads per sample, and PLUS, with 20 million sequencing reads per sample.

Even bulk sequencing data can be noisy. For downstream analysis, it is usually wise to have triplicates or at least duplicates. In any case, we always recommend you include at least a second vial for each of the samples you send, to make sure we have a technical back-up.

We use BWA or STAR for mapping the data and DEseq2 for differential gene expression analysis.

We use BWA or STAR for mapping the data and DEseq2 for differential gene expression analysis.

Not sure if bulk RNA sequencing is right for your project? Explore our other services.


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Full-length, total RNA single-cell sequencing platform.

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Ready to proceed? Use the form below to download pricing information on our RNA sequencing services.


Julia Strengers

Account Manager

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