Comparative analysis of sequencing technologies platforms for single-cell transcriptomics

Natarajan, K. N.; Miao, Z.; Jiang, M.; Huang, X.; Zhou, H.; Xie, J.; Wang, C.; Qin, S.; Zhao, Z.; Wu, L.; Li, B.; Hou, Y.; Liu, S.; Teichmann, S.

doi:10.1101/463117

bioRxiv · 10.1101/463117

Comparative analysis of sequencing technologies platforms for single-cell transcriptomics

Natarajan, K. N.·Miao, Z.·Jiang, M.·Huang, X.·Zhou, H.·Xie, J.·Wang, C.·Qin, S.·Zhao, Z.·Wu, L.·Li, B.·Hou, Y.·Liu, S.·Teichmann, S.

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Abstract

All single-cell RNA-seq protocols and technologies require library preparation prior to sequencing on a platform such as Illumina. Here, we present the first report to utilize the BGISEQ-500 platform for scRNA-seq, and compare the sensitivity and accuracy to Illumina sequencing. We generate a scRNA-seq resource of 468 unique single-cells and 1,297 matched single cDNA samples, performing SMARTer and Smart-seq2 protocols on mESCs and K562 cells with RNA spike-ins. We sequence these libraries on both BGISEQ-500 and Illumina HiSeq platforms using single- and paired-end reads. The two platforms have comparable sensitivity and accuracy in terms of quantification of gene expression, and low technical variability. Our study provides a standardised scRNA-seq resource to benchmark new scRNA-seq library preparation protocols and sequencing platforms.

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Natarajan, K. N., Miao, Z., Jiang, M., Huang, X., Zhou, H., Xie, J., Wang, C., Qin, S., Zhao, Z., Wu, L., Li, B., Hou, Y., Liu, S., Teichmann, S.. 2018-11-05. Comparative analysis of sequencing technologies platforms for single-cell transcriptomics. https://doi.org/10.1101/463117

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