Optimized single-cell RNA sequencing protocol to study early genome activation in mammalian preimplantation development

Here, we present a modification of single-cell tagged reverse transcription protocol to study gene expression on a single-cell level or with limited RNA input. We describe different enzymes for reverse transcription and cDNA amplification, modified lysis buffer, and additional clean-up steps before cDNA amplification. We also detail an optimized single-cell RNA sequencing method for handpicked single cells, or tens to hundreds of cells, as input material to study mammalian preimplantation development. For complete details on the use and execution of this protocol, please refer to Ezer et al.1

Automated summary

This article presents a modified single-cell tagged reverse transcription protocol for studying gene expression at the single-cell level or with limited RNA input. The authors describe various enzymes, a modified lysis buffer, and additional clean-up steps before cDNA amplification. They also provide an optimized single-cell RNA sequencing method for studying mammalian preimplantation development using handpicked single cells or tens to hundreds of cells as input material. For complete details on the use and execution of this protocol, please refer to Ezer et al.1.