ChIP-Seq Resources at the ENCODE Portal:

The Encyclopedia of DNA Elements (ENCODE) Project is a collaborative effort to create a catalog of genomic annotations in the human and mouse genomes by surveying the binding site of DNA-binding proteins and RNA-binding proteins as well as examining the transcriptional landscape and chromatin structure. The ENCODE Data Coordination Center has developed a comprehensive web portal ( for viewing and analysing the results of the ENCODE and Epigenomic Roadmap projects. Included in the corpus of ENCODE data are raw and processed data files from ChIP-seq, RNA-seq, DNase-seq, and other modern genomic techniques. Within the ENCODE consortium, ChIP-seq experiment protocols, quality metrics, and data analysis methodologies have been standardized so that results from different laboratories can be compared directly. Furthermore, ENCODE has implemented the data analysis pipelines in a form that can be replicated by anyone on ENCODE data, data from other projects, data from the literature and public databases, as well as data from new ChIP-seq experiments. All of the code is open-source, and the analysis pipelines are deployed on a cloud computing platform. Users are guaranteed that the quality metrics and results from their analyses are directly comparable to any data processed through the uniform ENCODE pipeline. 

Workshop Materials

To participate, you will need:


Cricket Sloan has been wrangling ENCODE data since 2010, first at the UCSC Genome Browser and then working with the Cherry Lab at Stanford. She is focused on data curation, standardization and reproducibility.  She is the Data Wrangler manager for ENCODE, GGR and modERN.  She has been deeply involved in importing data from the Roadmap Epigenomics Mapping Consortium.

Workshop Details

Date: Friday, May 12
Time: 10:30am – 1:30pm
Location: Collaboratory Classroom  (Boyer Hall, 529)
Seats Available: 28