Comparative analysis of sequencing technologies for single-cell transcriptomics

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Single-cell RNA sequencing (scRNA-seq) is crucial for understanding cellular heterogeneity.
• Library preparation is a necessary step before sequencing in scRNA-seq workflows.
• Evaluating different sequencing platforms is essential for optimizing scRNA-seq experiments.

Purpose of the Study:

• To compare the performance of the BGISEQ-500 and Illumina HiSeq platforms for scRNA-seq.
• To assess the sensitivity, accuracy, and technical variability of gene expression quantification on both platforms.
• To create a standardized scRNA-seq resource for benchmarking future protocols and platforms.

Main Methods:

• Generated a resource of 468 single cells and 1297 matched single cDNA samples.
• Applied SMARTer and Smart-seq2 library preparation protocols to two cell lines with RNA spike-ins.
• Sequenced libraries on both BGISEQ-500 and Illumina HiSeq platforms using single- and paired-end reads.

Main Results:

• BGISEQ-500 and Illumina HiSeq platforms showed comparable sensitivity for gene expression quantification.
• Both platforms exhibited similar accuracy in quantifying gene expression levels.
• Low technical variability was observed across both sequencing platforms.

Conclusions:

• The BGISEQ-500 platform is a viable and cost-effective alternative to Illumina HiSeq for scRNA-seq.
• The generated resource can serve as a benchmark for new scRNA-seq library preparation protocols and sequencing technologies.
• Standardized comparisons are vital for advancing the field of single-cell genomics.