Protocol for capturing a full transcriptome from single preimplantation embryos using So-Smart-seq
Summary: 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 inf...
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| Language: | English |
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Elsevier
2025-03-01
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| Series: | STAR Protocols |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166724007056 |
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| author | Chunyao Wei Jeannie T. Lee |
| author_facet | Chunyao Wei Jeannie T. Lee |
| author_sort | Chunyao Wei |
| collection | DOAJ |
| description | Summary: 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 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| format | Article |
| id | doaj-art-6d8afcfa7c47427294cecb3080daf5ee |
| institution | Kabale University |
| issn | 2666-1667 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj-art-6d8afcfa7c47427294cecb3080daf5ee2025-01-05T04:28:40ZengElsevierSTAR Protocols2666-16672025-03-0161103540Protocol for capturing a full transcriptome from single preimplantation embryos using So-Smart-seqChunyao Wei0Jeannie T. Lee1Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Corresponding authorDepartment of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Corresponding authorSummary: 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 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166724007056BioinformaticsDevelopmental biologyGeneticsGenomicsMolecular BiologySystems biology |
| spellingShingle | Chunyao Wei Jeannie T. Lee Protocol for capturing a full transcriptome from single preimplantation embryos using So-Smart-seq STAR Protocols Bioinformatics Developmental biology Genetics Genomics Molecular Biology Systems biology |
| title | Protocol for capturing a full transcriptome from single preimplantation embryos using So-Smart-seq |
| title_full | Protocol for capturing a full transcriptome from single preimplantation embryos using So-Smart-seq |
| title_fullStr | Protocol for capturing a full transcriptome from single preimplantation embryos using So-Smart-seq |
| title_full_unstemmed | Protocol for capturing a full transcriptome from single preimplantation embryos using So-Smart-seq |
| title_short | Protocol for capturing a full transcriptome from single preimplantation embryos using So-Smart-seq |
| title_sort | protocol for capturing a full transcriptome from single preimplantation embryos using so smart seq |
| topic | Bioinformatics Developmental biology Genetics Genomics Molecular Biology Systems biology |
| url | http://www.sciencedirect.com/science/article/pii/S2666166724007056 |
| work_keys_str_mv | AT chunyaowei protocolforcapturingafulltranscriptomefromsinglepreimplantationembryosusingsosmartseq AT jeannietlee protocolforcapturingafulltranscriptomefromsinglepreimplantationembryosusingsosmartseq |