In the last four years the ZENCODE-ITN project has fulfilled its key objectives in recruitment and training of 15 early stage researchers, setting up and utilising network communication channels, a website and student network via social media. The progress and results of the network activities were communicated via two international conferences, presentations at independent scientific meetings and peer reviewed publications. All due deliverables have been submitted and expected milestones completed. Seven successful training events have been organised including several mastercourses and transferable skills training events.
We have made substantial progress in the following scientific objectives:
Computational tools development:
- new data mining tool is in development for analysing in which tissues and when during development genes work
- we established a Data Coordination Centre (DCC) for collecting and standardizing zebrafish epigenome, transcriptome datasets,
- Software and data structures for anatomy specific gene expression analysis has been developed
- Computational pipeline has been created to compare spatio-temporal expression profiles and to identify co-expression groups
- genomics data visualisation tools have been developed for visualising multidimensional datasets
Experimental technology development and data collection:
- We have collected genome wide epigenetic data from a variety of tissues and cell types including primordial germ cells, pancreatic cell types, endoderm, muscle and nervous system
- We have developed new miniaturized biochemical techniques to collect genome wide data from small cell numbers (e.g. chromatin immunoprecipitation, promoter capture technology- CAGE and chromosome conformation capture assay)
- We have collected human non-coding functional elements for pancreatic islets to then study their function in a fish embryo model
Genome wide data annotation:
- ZENCODE-ITN partners progressed substantially with the comprehensive annotation of the zebrafish genome by seeding and leading the efforts of a global consortium effort under the umbrella of DANIO-CODE.
- ZENCODE-ITN members have played central and dominant role in initiating, establishing, coordinating managing and undertaking DANIO-CODE objectives (
http://www.birmingham.ac.uk/generic/danio-code/data-coordination-centre.aspx(opens in new window))
- We have generated a catalog and classification of so called non-coding RNAs in nuclear and cytoplasmic fractions of developing embryos at various stages
- We have analysed sequence variants of human disease associated non-coding DNA elements which are predicted to regulate gene activity
- We have characterised the epigenetic landscape of primordial germ cells and identified key
- We have characterised transcription regulatory networks in endoderm development and pancreatic islet specification
- We have characterised zebrafish mutants affecting muscle development
by transcriptome analysis
