RNA-seq in the tetraploid Xenopus laevis enables genome-wide insight in a classic developmental biology model organism.

No abstract is available for this paper.

• Publication year

  2014

• Venue

  Methods

• Publication date

  2014-04-01

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1016/j.ymeth.2013.06.009PMID 23792920PMCID PMC3884041
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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  2000cited by this paper
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  1994cited by this paper
• Ordering gene function: the interpretation of epistasis in regulatory hierarchies.

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• Mutations affecting segment number and polarity in Drosophila

  1980cited by this paper
• Specific-locus test shows ethylnitrosourea to be the most potent mutagen in the mouse.

  1979cited by this paper
• The genetics of Caenorhabditis elegans.

  1974cited by this paper
• Synthetic Spike-in Standards for Rna-seq Experiments Material Supplemental Open Access License Commons Creative

  year unknowncited by this paper

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