ENCODE project

The ENCODE project aims to define all functional elements of the human genome... 

Many of these unanticipated RNA transcripts have been identified. Some of these derive from regions of the genome previously considered to be transcriptionally silent. Still others overlap protein-coding regions. The ENCODE project compares functional DNA elements from man, monkey, and mouse. Novel evolutionary relationships are certain to result. ENCODE is early but it promises great new insights into how the genome works. 

The Encode Project Consortium (2007) Identification and analysis of functional elements in 1% of the human genome by... 

ENCODE Project Consortium. The ENCODE(ENCyclopedia Of DNA Elements) Project. Science 2004 306(5696) 636-640. 

The earliest MRI method, projection imaging, relied on the acquisition of a series of frequency-encoded projections of the subject at successive angles followed by reconstruction of the set of projections into an image. 

The ENCODE project has produced standards for RNA-Seq. Two important considerations are worth mentioning. First, it is important to include controls for RNA-Seq experiments. One type of control are spike-in controls that have been produced by the External RNA Controls Consortium (53). Spike-in controls consist of foreign or synthetic RNAs of known abundance that are put into the RNA cocktail before fractionation. These spike-ins provide an important control because the measurements produced from the RNA-Seq experiment can be compared to known inputs. While it is difficult to standardize target transcriptome measurements based on 96 synthetic RNAs that have different sequence characteristics, they are extremely useful as quality control checks for RNA-Seq experiments (55). 

Genome Bioinformatics Site. University of California, Santa Cruz (UCSC). URL http //genome.ucsc.edu/. Contains the reference sequence and working draft assemblies for a large collection of genomes. Provides a portal to the Encyclopedia of DNA Elements (ENCODE) project. 

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