ZENCODE-ITN SIGNED
Computational and functional annotation of genomic elements during development of the model vertebrate zebrafish
Total Cost €
0EC-Contrib. €
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Explore the words cloud of the ZENCODE-ITN project. It provides you a very rough idea of what is the project "ZENCODE-ITN" about.
Project "ZENCODE-ITN" data sheet
The following table provides information about the project.
| Coordinator |
THE UNIVERSITY OF BIRMINGHAM
Organization address contact info |
| Coordinator Country | United Kingdom [UK] |
| Project website | http://www.birmingham.ac.uk/zencode-itn |
| Total cost | 3˙724˙035 € |
| EC max contribution | 3˙724˙035 € (100%) |
| Programme |
1. H2020-EU.1.3.1. (Fostering new skills by means of excellent initial training of researchers) |
| Code Call | H2020-MSCA-ITN-2014 |
| Funding Scheme | MSCA-ITN-ETN |
| Starting year | 2015 |
| Duration (year-month-day) | from 2015-01-01 to 2018-12-31 |
Partnership
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Project objective
The recent explosion of next generation sequencing (NGS) data has caught Europe unprepared and led to a critical shortage of computational biology expertise. As NGS methods are expected to become pervasive from basic science to personalised medicine there is an urgent need for highly skilled young scientists trained in both computational biology and experimental wet lab biology. Our network addresses this important problem of the postgenomic era. We aim to provide multi-disciplinary skills for a solid foundation in computational biology and developmental genomics. Developmental genomics is central to understanding of ontogeny and many genetic and congenital anomalies, but was outside the scope of the landmark ENCODE and FANTOM projects. ENCODE highlighted the need for an in vivo vertebrate model that enables high throughput in vivo functional testing of hypotheses generated from genome scale annotation. Zebrafish is an ideal model for extending the scope of genomics to vertebrate development. We aim to comprehensively annotate functional elements, decipher genomic codes of transcription, as well as coding and non-coding gene function during development and enhance zebrafish as an attractive developmental, comparative and disease model. The participants include 7 non-academic members (2 of which are beneficiaries), major zebrafish genomics laboratories, eminent computational biologists and world class genomics technology experts active in FANTOM and ENCODE. The training program involves 15 ESRs, more than 40 intersectoral and interdisciplinary secondments totalling 19 months, 7 training courses and 2 workshops/conferences. The main outcome of this programme is a cohort of researchers with computational, experimental laboratory and transferable skills ready to further their career in academia, public health and the private sector.
Deliverables
| Gene expression datasets | Documents, reports | 2019-06-19 13:01:03 |
| Manuscript preparation | Documents, reports | 2019-06-19 13:01:03 |
| Verification of sequence variants | Documents, reports | 2019-06-19 13:01:03 |
| Analysis of transcriptome datasets, including non-coding elements | Documents, reports | 2019-06-19 13:01:03 |
| Public Engage | Other | 2019-06-19 13:01:03 |
| Software packages | Demonstrators, pilots, prototypes | 2019-06-19 13:01:03 |
| ChIP-seq datasets | Documents, reports | 2019-06-19 13:01:03 |
| Low cell number and single cell protocols | Documents, reports | 2019-06-19 13:01:04 |
| Establishment of curated high quality zebrafish sequence data repository. | Documents, reports | 2019-06-19 13:01:04 |
| Website | Websites, patent fillings, videos etc. | 2019-06-19 13:01:02 |
Take a look to the deliverables list in detail: detailed list of ZENCODE-ITN deliverables.
Publications
| year | authors and title | journal | last update |
|---|---|---|---|
| 2018 |
Swarnima Joshi, Sanamjeet Virdi, Christelle Etard, Robert Geisler, Uwe Strähle Mutation of a serine near the catalytic site of the choline acetyltransferase a gene almost completely abolishes motility of the zebrafish embryo published pages: e0207747, ISSN: 1932-6203, DOI: 10.1371/journal.pone.0207747 |
PLOS ONE 13/11 | 2019-06-19 |
| 2018 |
Clemens B. Hug, Juan M. Vaquerizas The Birth of the 3D Genome during Early Embryonic Development published pages: 903-914, ISSN: 0168-9525, DOI: 10.1016/j.tig.2018.09.002 |
Trends in Genetics 34/12 | 2019-06-19 |
| 2017 |
Hyun-Woo Jeong, BenjamÃn Hernández-RodrÃguez, JungMo Kim, Kee-Pyo Kim, Rocio Enriquez-Gasca, Juyong Yoon, Susanne Adams, Hans R. Schöler, Juan M. Vaquerizas, Ralf H. Adams Transcriptional regulation of endothelial cell behavior during sprouting angiogenesis published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-017-00738-7 |
Nature Communications 8/1 | 2019-06-19 |
| 2016 |
Kai Kruse, Clemens B. Hug, BenjamÃn Hernández-RodrÃguez, Juan M. Vaquerizas TADtool: visual parameter identification for TAD-calling algorithms published pages: 3190-3192, ISSN: 1367-4803, DOI: 10.1093/bioinformatics/btw368 |
Bioinformatics 32/20 | 2019-06-19 |
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The information about "ZENCODE-ITN" are provided by the European Opendata Portal: CORDIS opendata.