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Computational and functional annotation of genomic elements during development of the model vertebrate zebrafish

Deliverables

ChIP-seq datasets

Datasets for specific TF and histones modification in the developing zebrafish embryo.

Gene expression datasets

CAGE RNA-seq datasets for the early zebrafish embryo

Manuscript preparation

ESR16 together with ESR15 will write a manuscript for publication to open the DCC data, for example in the “Scientific Data” journal. due date: manuscript for submission ready November 2018

Low cell number and single cell protocols

Methods to profile epigenome and transcriptome of low cell number populations and single cells

Analysis of transcriptome datasets, including non-coding elements

RNA-seq datasets from zebrafish developmental transitions, including lncRNAs and mobile genomic elements.

Verification of sequence variants

Reports on functional validation of zebrafish and human sequence variants

Establishment of curated high quality zebrafish sequence data repository.

ESR3 and ESR14 collected zebrafish sequencing data from the ZENCODE-ITN members together with structured data annotation. The pilot study showed that scaling up of this effort toward the whole zebrafish community will require large efforts for the curation of the collected data and the collected data annotation. ESR15 as research assistant will conduct the careful data annotation which will facilitate the establishment of the most comprehensive zebrafish sequencing data repository

Public Engage

Hold public open day on genomics

Website

Network website online for communication

Software packages

Software for detecting and classify genomic elements and characteristics, including in single cells, and for integration and visualization of data sets

Searching for OpenAIRE data...

Publications

Mutation of a serine near the catalytic site of the choline acetyltransferase a gene almost completely abolishes motility of the zebrafish embryo

Author(s): Swarnima Joshi, Sanamjeet Virdi, Christelle Etard, Robert Geisler, Uwe Strähle
Published in: PLOS ONE, Issue 13/11, 2018, Page(s) e0207747, ISSN 1932-6203
DOI: 10.1371/journal.pone.0207747

Transcriptional regulation of endothelial cell behavior during sprouting angiogenesis

Author(s): Hyun-Woo Jeong, Benjamín Hernández-Rodríguez, JungMo Kim, Kee-Pyo Kim, Rocio Enriquez-Gasca, Juyong Yoon, Susanne Adams, Hans R. Schöler, Juan M. Vaquerizas, Ralf H. Adams
Published in: Nature Communications, Issue 8/1, 2017, ISSN 2041-1723
DOI: 10.1038/s41467-017-00738-7

The Birth of the 3D Genome during Early Embryonic Development

Author(s): Clemens B. Hug, Juan M. Vaquerizas
Published in: Trends in Genetics, Issue 34/12, 2018, Page(s) 903-914, ISSN 0168-9525
DOI: 10.1016/j.tig.2018.09.002

TADtool: visual parameter identification for TAD-calling algorithms

Author(s): Kai Kruse, Clemens B. Hug, Benjamín Hernández-Rodríguez, Juan M. Vaquerizas
Published in: Bioinformatics, Issue 32/20, 2016, Page(s) 3190-3192, ISSN 1367-4803
DOI: 10.1093/bioinformatics/btw368