Bulk RNA sequencing

High-quality transcriptome data

Our bulk RNA sequencing is based on single-cell chemistry, enabling low-input sequencing.

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Features of bulk RNA sequencing

Detect transcriptome profiles in populations

Bulk RNA sequencing is the method of choice for transcriptomic analysis of pooled cell populations, tissue sections, and biopsies. It measures the average expression level of individual genes across hundreds to millions of input cells to produce a global idea of gene expression differences between samples.

We use the same CEL-Seq2–style barcodes and reagents as for our SORT-seq technology to enable sample multiplexing. Each sample gets its own sample-specific barcode, which allows us to pool multiple samples into one sequencing library. Our use of single-cell sequencing reagents allows us to process bulk samples with as few as 100 cells as input.

The ability to process even very low–input samples can sometimes make the difference when you are investigating rare cell types, are interested in select populations, or require a complex experimental design with few surviving cells. We have performed bulk RNA-seq on more than twenty different species and we are experienced with various tissue types, from cultured dendritic cells to transgenic brain tumors and from intestinal organoids to microalgae.


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.


Available for low input

Because we use single-cell reagents, we can perform a bulk RNA sequencing analysis on extremely low sample volumes. We need only 100 cells for bulk RNA sequencing. 

Combine multiple samples in one sequencing library 

Our ability to multiplex samples means we can speed up turnaround times and enhance the processing efficiency of large amounts of samples.

Step 1 - Consultation with our clients
Step 1


Every project starts with one or more free consultations because no two single-cell projects are the same. Our experienced PhD-level team discusses your biological question, sample type, planning, data analysis options, and other wishes. This will ensure you select the best method for your project and can hit the ground running.

Meet our experts

Scientist performing single cell sequencing experiments at Single Cell Discoveries
Step 2

Sample Preparation

You can decide to perform RNA purification yourself or outsource it to our laboratory. Check the sample requirements for details on both options.

Sample requirementsShipping information

Single cell sequencing Illumina NovaSeq scientist places samples in the new NovaSeq X machine
Step 3

Processing in Our Lab

Our experienced team performs the bulk RNA sequencing protocol in our lab. We sequence the libraries on our Illumina NovaSeq X Plus or NextSeq 2000. We'll do multiple QC checks and keep you informed of the status of your project.

Sample and library QC

Step 4 - Analysis of sequencing data
Step 4

Data Analysis

Our data team performs data quality checks and discusses irregularities with our lab team if necessary. You will receive the raw data files, data report, and a guiding explanation. Talk to our data consulting team for help or request additional investigations such as gene set enrichment analysis and deconvolution of cell type abundances.

Our data analysisView exploratory report


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

  • Regular updates during sample processing, including QC
  • Raw sequencing data (FASTQ files)
  • Gene count tables
  • QC report of mapping results (raw and mapped reads per sample, and PCA plot)
  • An explanation from our data team about data quality metrics
  • All raw sequencing data, results and reports are processed on EU servers, and securely encrypted using an AES (Advanced Encryption Standard) algorithm with a 256-bit key, before being delivered to the customers and archived.
Information Guide preview: 10x Genomics

Bulk RNA sequencing
Information Guide

Get an overview of Single Cell Discoveries, bulk RNA sequencing, how to get started, and more in our bulk RNA sequencing information guide.


Recent publications using bulk RNA sequencing

How deep should I sequence my samples?

Sequencing depth depends on the number of samples, your budget, and your biological question. We offer two packages for bulk RNA sequencing: STANDARD, with 10 million sequencing reads per sample, and PLUS, with 20 million sequencing reads per sample.

Information Guide

Discover our bulk RNA sequencing service

Download our information guide to access an overview of Single Cell Discoveries, explore our bulk RNA sequencing service, learn how to get started, and gain more valuable insights.