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

Project Information

ZENCODE-ITN

Grant agreement ID: 643062

DOI 10.3030/643062

Project closed

EC signature date 18 December 2014

Start date 1 January 2015

End date 31 December 2018

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost € 3 724 035,89

EU contribution € 3 724 035,89

Coordinated by

THE UNIVERSITY OF BIRMINGHAM
United Kingdom

Deliverables

Documents, reports (7)

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

Other (1)

Public Engage

Hold public open day on genomics

Websites, patent fillings, videos etc. (1)

Website

Network website online for communication

Demonstrators, pilots, prototypes (1)

Software packages

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

Publications

Peer reviewed articles (4)

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
Publisher: Public Library of Science
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
Publisher: Nature Publishing Group
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
Publisher: Elsevier BV
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
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btw368