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Opendata, web and dolomites

ZENCODE-ITN SIGNED

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

Total Cost €

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EC-Contrib. €

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Partnership

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Outcomes and
results

ZENCODE-ITN project word cloud

Explore the words cloud of the ZENCODE-ITN project. It provides you a very rough idea of what is the project "ZENCODE-ITN" about.

training career cohort vertebrate attractive comprehensively transferable personalised ontogeny lab explosion annotate academic caught network basic fantom generation ngs months totalling genetic biology genome function genomics zebrafish interdisciplinary postgenomic laboratories genomic medicine anomalies encode annotation academia young courses health scope eminent members decipher public urgent 15 outside conferences solid congenital coding landmark skilled developmental beneficiaries codes central workshops skills world functional wet sequencing vivo ideal ready scientists private class experimental led throughput gene era laboratory foundation transcription active secondments intersectoral esrs computational unprepared outcome biologists 19 critical disciplinary expertise pervasive trained hypotheses disease highlighted science experts data model shortage

Project "ZENCODE-ITN" data sheet

The following table provides information about the project.

Coordinator	THE UNIVERSITY OF BIRMINGHAM Organization address address: Edgbaston city: BIRMINGHAM postcode: B15 2TT website: www.bham.ac.uk contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.
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

Take a look of project's partnership.

#	participants	country	role	EC contrib. [€]
1	THE UNIVERSITY OF BIRMINGHAM THE UNIVERSITY OF BIRMINGHAM Organization address address: Edgbaston city: BIRMINGHAM postcode: B15 2TT website: www.bham.ac.uk contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	UK (BIRMINGHAM)	coordinator	546˙575.00
2	KAROLINSKA INSTITUTET KAROLINSKA INSTITUTET Organization address address: Nobels Vag 5 city: STOCKHOLM postcode: 17177 website: www.ki.se contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	SE (STOCKHOLM)	participant	769˙006.00
3	UNIVERSITE DE LIEGE UNIVERSITE DE LIEGE Organization address address: PLACE DU 20 AOUT 7 city: LIEGE postcode: 4000 website: www.ulg.ac.be contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	BE (LIEGE)	participant	501˙120.00
4	KARLSRUHER INSTITUT FUER TECHNOLOGIE KARLSRUHER INSTITUT FUER TECHNOLOGIE Organization address address: KAISERSTRASSE 12 city: KARLSRUHE postcode: 76131 website: www.kit.edu contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	DE (KARLSRUHE)	participant	498˙432.00
5	KING'S COLLEGE LONDON KING'S COLLEGE LONDON Organization address address: STRAND city: LONDON postcode: WC2R 2LS website: www.kcl.ac.uk contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	UK (LONDON)	participant	447˙888.00
6	MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV Organization address address: HOFGARTENSTRASSE 8 city: MUENCHEN postcode: 80539 website: n.a. contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	DE (MUENCHEN)	participant	387˙670.00
7	IMPERIAL COLLEGE OF SCIENCE TECHNOLOGY AND MEDICINE IMPERIAL COLLEGE OF SCIENCE TECHNOLOGY AND MEDICINE Organization address address: SOUTH KENSINGTON CAMPUS EXHIBITION ROAD city: LONDON postcode: SW7 2AZ website: http://www.imperial.ac.uk/ contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	UK (LONDON)	participant	273˙287.00
8	CONSORCI INSTITUT D'INVESTIGACIONS BIOMEDIQUES AUGUST PI I SUNYER CONSORCI INSTITUT D'INVESTIGACIONS BIOMEDIQUES AUGUST PI I SUNYER Organization address address: CALLE ROSSELLO 149 PUERTA BJS city: BARCELONA postcode: 8036 website: http://www.idibaps.org/en_index.html contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	ES (BARCELONA)	participant	247˙872.00
9	RIKEN THE INSTITUTE OF PHYSICAL ANDCHEMICAL RESEARCH RIKEN THE INSTITUTE OF PHYSICAL ANDCHEMICAL RESEARCH Organization address address: HIROSAWA 2-1 city: WAKO SHI SAITAMA postcode: 351 0198 website: n.a. contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	JP (WAKO SHI SAITAMA)	participant	52˙181.00
10	BGI EUROPE INSTITUTE FOND BGI EUROPE INSTITUTE FOND Organization address address: OLE MAALOES VEJ 3 city: KOBENHAVN N postcode: 2200 website: n.a. contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	DK (KOBENHAVN N)	participant	0.00
11	GENOME RESEARCH LIMITED GENOME RESEARCH LIMITED Organization address address: THE GIBBS BUILDING, EUSTON ROAD 215 city: LONDON postcode: NW1 2BE website: http://www.sanger.ac.uk contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	UK (LONDON)	participant	0.00
12	D Young & Co LLP D Young & Co LLP Organization address address: n.a. city: London postcode: n.a. website: n.a. contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	UK (London)	partner	0.00
13	MicroDiscovery GmbH MicroDiscovery GmbH Organization address address: MARIENBURGER STRASSE 1 city: BERLIN postcode: 10405 website: www.microdiscovery.de contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	DE (BERLIN)	partner	0.00
14	Skillstudio Limited Skillstudio Limited Organization address address: n.a. city: Chislehurst postcode: n.a. website: n.a. contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	UK (Chislehurst)	partner	0.00
15	Zebrafish Model Organism Database Zebrafish Model Organism Database Organization address address: n.a. city: Eugene postcode: n.a. website: n.a. contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	US (Eugene)	partner	0.00

Map

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

List of 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

List of publications.
year	authors and title	journal	last update
2018	Swarnima Joshi, Sanamjeet Virdi, Christelle Etard, Robert Geisler, Uwe StrÃ¤hle 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 HernÃ¡ndez-RodrÃguez, JungMo Kim, Kee-Pyo Kim, Rocio Enriquez-Gasca, Juyong Yoon, Susanne Adams, Hans R. SchÃ¶ler, 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 HernÃ¡ndez-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.

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