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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).
Akkers,
A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos.
2009, Pubmed,
Xenbase
Akkers,
A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos.
2009,
Pubmed
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Xenbase
Boyle,
High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.
2011,
Pubmed
Briggs,
The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution.
2018,
Pubmed
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Xenbase
Bright,
Assay for Transposase-Accessible Chromatin-Sequencing Using Xenopus Embryos.
2019,
Pubmed
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Xenbase
Buenrostro,
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Pubmed
Chen,
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Pubmed
Chiu,
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2014,
Pubmed
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Xenbase
Cho,
DNase-seq to Study Chromatin Accessibility in Early Xenopus tropicalis Embryos.
2019,
Pubmed
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Xenbase
Cusanovich,
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2018,
Pubmed
Elurbe,
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2017,
Pubmed
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Xenbase
Gentsch,
Mapping Chromatin Features of Xenopus Embryos.
2019,
Pubmed
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Xenbase
Gentsch,
In vivo T-box transcription factor profiling reveals joint regulation of embryonic neuromesodermal bipotency.
2013,
Pubmed
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Xenbase
Gilchrist,
Transcriptomics and Proteomics Methods for Xenopus Embryos and Tissues.
2020,
Pubmed
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Xenbase
Hellsten,
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2010,
Pubmed
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Xenbase
Hontelez,
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2019,
Pubmed
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Xenbase
Hontelez,
Embryonic transcription is controlled by maternally defined chromatin state.
2015,
Pubmed
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Xenbase
Jäger,
Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci.
2015,
Pubmed
Kalhor,
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2011,
Pubmed
Kaya-Okur,
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Pubmed
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2019,
Pubmed
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Xenbase
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2016,
Pubmed
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Xenbase
Neph,
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Pubmed
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Pubmed
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Endodermal Maternal Transcription Factors Establish Super-Enhancers during Zygotic Genome Activation.
2019,
Pubmed
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Xenbase
Quigley,
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2019,
Pubmed
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Xenbase
Quigley,
Rfx2 Stabilizes Foxj1 Binding at Chromatin Loops to Enable Multiciliated Cell Gene Expression.
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Pubmed
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Xenbase
Rozenblatt-Rosen,
The Human Cell Atlas: from vision to reality.
2017,
Pubmed
Savova,
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2017,
Pubmed
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Xenbase
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2016,
Pubmed
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Xenbase
Song,
DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells.
2010,
Pubmed
Thélie,
Prdm12 specifies V1 interneurons through cross-repressive interactions with Dbx1 and Nkx6 genes in Xenopus.
2015,
Pubmed
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Xenbase
Yasuoka,
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2014,
Pubmed
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Xenbase
Yoon,
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Pubmed
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Xenbase
van Heeringen,
Nucleotide composition-linked divergence of vertebrate core promoter architecture.
2011,
Pubmed
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Xenbase
