Protocol for capturing a full transcriptome from single preimplantation embryos using So-Smart-seq

Chunyao Wei; Jeannie T Lee

doi:10.1016/j.xpro.2024.103540

Protocol for capturing a full transcriptome from single preimplantation embryos using So-Smart-seq

STAR Protoc. 2025 Jan 4;6(1):103540. doi: 10.1016/j.xpro.2024.103540. Online ahead of print.

Authors

Chunyao Wei¹, Jeannie T Lee²

Affiliations

¹ Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Electronic address: weic@molbio.mgh.harvard.edu.
² Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Electronic address: lee@molbio.mgh.harvard.edu.

PMID: 39756032
DOI: 10.1016/j.xpro.2024.103540

Abstract

Strand-optimized Smart-seq (So-Smart-seq) can capture a comprehensive transcriptome from low-input samples. This technique detects both polyadenylated and non-polyadenylated RNAs, inclusive of repetitive RNAs, while excluding highly abundant ribosomal RNAs. So-Smart-seq preserves strand information and minimizes 5' to 3' coverage bias. We describe steps for the analysis of single mouse preimplantation embryos, including embryo isolation, library preparation, ribosomal cDNA depletion, and initial data processing. The protocol may be adapted for other low-input samples and the detection of small RNAs of <200 nt. For complete details on the use and execution of this protocol, please refer to Wei et al.¹.

Keywords: Bioinformatics; Developmental biology; Genetics; Genomics; Molecular Biology; Systems biology.