Genomics Methods for Xenopus Embryos and Tissues | Zendy

Michael J. Gilchrist | Zendy; Ken W.Y. Cho | Zendy; Gert Jan C. Veenstra | Zendy

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Genomics Methods for Xenopus Embryos and Tissues

Author(s) -

Michael J. Gilchrist,

Ken W.Y. Cho,

Gert Jan C. Veenstra

Publication year - 2020

Publication title -

cold spring harbor protocols

Language(s) - English

Resource type - Journals

eISSN - 1940-3402

pISSN - 1559-6095

DOI - 10.1101/pdb.top097915

Subject(s) - chromatin , chromatin immunoprecipitation , dna sequencing , xenopus , chip sequencing , genomic dna , biology , computational biology , massive parallel sequencing , genomics , dna , sequencing by ligation , transposase , genome , genetics , genomic library , gene , chromatin remodeling , transposable element , base sequence , promoter , gene expression

High-throughput sequencing methods have created exciting opportunities to explore the regulatory landscape of the entire genome. Here we introduce methods to characterize the genomic locations of bound proteins, open chromatin, and sites of DNA–DNA contact in Xenopus embryos. These methods include chromatin immunoprecipitation followed by sequencing (ChIP-seq), a combination of DNase I digestion and sequencing (DNase-seq), the assay for transposase-accessible chromatin and sequencing (ATAC-seq), and the use of proximity-based DNA ligation followed by sequencing (Hi-C).

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