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Course on Access to ENCODE data through the UCSC Genome Browser 2014


The CNIO Bioinformatics Unit is organising a Course on Access to ENCODE data through the UCSC Genome Browser, to be held on Monday, June 9th 2014.

Please contact us (This email address is being protected from spambots. You need JavaScript enabled to view it. ) in advance if you wish to attend the course.

Monday June 9th, "Access to ENCODE data through the UCSC Genome Browser"

The Encode project was devised to characterize all the functional elements in the human genome. It started with a pilot phase in 2003, where the consortium researchers studied the 1% of the genome. In 2007 they expanded this search to the full genome, in a second phase called the production phase. It was in september 2012 when all the results obtained from this second phase were published by the consortium in Nature, Genome Research and Genome Biology (
The investigations performed by the Encode consortium involved not only the human genome, but also the mouse genome, the fruit fly genome and the warm genome.

Encode took advantage of the last sequencing technologies to perform global studies across the genome, including the creation of the most complete annotation set of genes and gene isoforms (coding genes, ncRNAs and pseudogenes), studies that measured transcriptional levels of genes (polyA +, polyA -) in a strand specif manner, experiments that analyzed the structure and remodeling of chromatin based on chemical modifications in histones (methylation and acetylation of specific residues) and the presence of DNA hypersensitivity sites, characterization of specific sites for transcription factor binding, determination of targets for certain RNA binding proteins, DNA methylation levels, variations in copy number of DNA segments, characterization of transcription start sites, subcelular localization of RNAs and more.
All of these experiments were performed on a battery of more than 147 cell types, divided in three different categories.

While the Encode investigations were taking place, huge amounts of data were continuously generated. The entity that was designated as the data coordination center for human and mouse data was the UCSC Genome Browser.

This course focuses on how to access the information generated by Encode. Learn how the information is structured and how to download bulk files with data from the different experiments, or how to select pieces of Encode data from specific regions in the genome.



Osvaldo Graña and David G. Pisano, Bioinformatics Unit (CNIO)

Course Agenda (CNIO Auditorium)

10:00 Introduction to the ENCODE project

10:45 The UCSC Genome Browser and ENCODE: a general view

11:30 Coffee break

12:00 Hands-on exercise [download]

13:00 Lunch

14:30 Visualizing ENCODE data with the UCSC Genome Browser

15:30 Hands-on exercises [download exercise 1][download exercise 2]

16:30 Finish

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