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

Informazioni relative al progetto

ZENCODE-ITN

ID dell’accordo di sovvenzione: 643062

DOI 10.3030/643062

Progetto chiuso

Data della firma CE 18 Dicembre 2014

Data di avvio 1 Gennaio 2015

Data di completamento 31 Dicembre 2018

Finanziato da

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Costo totale € 3 724 035,89

Contributo UE € 3 724 035,89

Coordinato da

THE UNIVERSITY OF BIRMINGHAM
United Kingdom

Risultati finali

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

Pubblicazioni

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

Autori: Swarnima Joshi, Sanamjeet Virdi, Christelle Etard, Robert Geisler, Uwe Strähle
Pubblicato in: PLOS ONE, Numero 13/11, 2018, Pagina/e e0207747, ISSN 1932-6203
Editore: Public Library of Science
DOI: 10.1371/journal.pone.0207747

Transcriptional regulation of endothelial cell behavior during sprouting angiogenesis

Autori: 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
Pubblicato in: Nature Communications, Numero 8/1, 2017, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-017-00738-7

The Birth of the 3D Genome during Early Embryonic Development

Autori: Clemens B. Hug, Juan M. Vaquerizas
Pubblicato in: Trends in Genetics, Numero 34/12, 2018, Pagina/e 903-914, ISSN 0168-9525
Editore: Elsevier BV
DOI: 10.1016/j.tig.2018.09.002

TADtool: visual parameter identification for TAD-calling algorithms

Autori: Kai Kruse, Clemens B. Hug, Benjamín Hernández-Rodríguez, Juan M. Vaquerizas
Pubblicato in: Bioinformatics, Numero 32/20, 2016, Pagina/e 3190-3192, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btw368