ArticleMethods (San Diego, Calif.)2014
RNA-seq in the tetraploid Xenopus laevis enables genome-wide insight in a classic developmental biology model organism.
Article in Methods (San Diego, Calif.), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
12 citing papers in PubMed.
- Cellular and Molecular Triggers of Retinal Regeneration in Amphibians.Life (Basel, Switzerland) · 2023Review
- Review
- Article
- Engagement of Foxh1 in chromatin regulation revealed by protein interactome analyses.Development, growth & differentiation · 2022Article
- Studying In Vivo Retinal Progenitor Cell Proliferation in Xenopus laevis.Methods in molecular biology (Clifton, N.J.) · 2020Article
- Cross-species functional analyses reveal shared and separate roles for Sox11 in frog primary neurogenesis and mouse cortical neuronal differentiation.Biology open · 2016Article
- Functional Cloning Using a Xenopus Oocyte Expression System.Journal of visualized experiments : JoVE · 2016Article
- Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs.Nucleic acids research · 2014Article
- PrimerSeq: Design and visualization of RT-PCR primers for alternative splicing using RNA-seq data.Genomics, proteomics & bioinformatics · 2014Article
- Proteomic profiling of cardiac tissue by isolation of nuclei tagged in specific cell types (INTACT).Development (Cambridge, England) · 2014Article
- Optimizing plant transporter expression in Xenopus oocytes.Plant methods · 2013Article
- A Gro/TLE-NuRD corepressor complex facilitates Tbx20-dependent transcriptional repression.Journal of proteome research · 2013Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Advances in sequencing technology have significantly advanced the landscape of developmental biology research. The dissection of genetic networks in model and non-model organisms has been greatly enhanced with high-throughput sequencing technologies. RNA-seq has revolutionized the ability to perform developmental biology research in organisms without a published genome sequence. Here, we describe a protocol for developmental biologists to perform RNA-seq on dissected tissue or whole embryos. We start with the isolation of RNA and generation of sequencing libraries. We further show how to interpret and analyze the large amount of sequencing data that is generated in RNA-seq. We explore the abilities to examine differential expression, gene duplication, transcript assembly, alternative splicing and SNP discovery. For the purposes of this article, we use Xenopus laevis as the model organism to discuss uses of RNA-seq in an organism without a fully annotated genome sequence.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.