RNA sequencing is a technique used to analyze entire genomes by looking at the expression of their genes. Today, such genome-wide expression analyses are a standard tool for genomic studies because they rely on high-throughput technologies, which themselves have become widely available.
RNA sequencing is still expensive and time-consuming, but some new approaches have come in to solved this (propelled by the revolution in single-cell transcriptomic using the sample barcoding ). In this case, individual “barcode” sequences are added to each DNA fragment during library preparation so that each one can be identified and sorted before the analysis of the final data – meaning that this approach only requires a single library that contains multiple distinct samples or cells (instead of one library per sample for classic RNA sequencing).
This technics reduces both cost and time, and this could extend to bulk RNA sequencing of large sets of samples.
In 2019, EPFL bioengineers have developed a new method for Bulk RNA Sequencing called Bulk RNA Barcoding and sequencing (BRB-seq), which is 25 times less expensive than a conventional commercial RNA sequencing technology (Illumina’s TruSeq).
Figure 1: Illustration of the BRB-seq method. Credit: Daniel Alpern/EPFL
BRB-seq preserves strand-specificity and offers a low-cost approach for performing transcriptomics on hundreds of samples, which can increase the number of biological replicates (and therefore experimental accuracy) in a single run.
In terms of performance, the scientists found that BRB-seq can detect the same number of genes as “the gold standard” in the field, namely TruSeq Stranded mRNA, at the same sequencing depth and that the technique produces reliable data even with low-quality RNA samples. Moreover, it generates genome-wide transcriptomic data at a cost that is comparable to profiling four genes using RT-qPCR, which is currently a standard, but low-throughput method for measuring gene expression.
In a test, BRB-seq could generate ready-to-sequence genomic libraries for up to 192 samples a day, requiring only two hours of hands-on time. The technique combined with the genomics data analysis provided by SciLicium allowing result acquisition in a short time.