University of Washington Human Reference Epigenome Mapping Project (RNA-seq)

By (Secondary Ownership. The experiment uses only third-party data.)

THIS IS THE RNA-SEQ COMPONENT OF THE STUDY.

The human embryonic stem cells (hESCs) are a unique model system for investigating the mechanisms of human development due to their ability to replicate indefinitely while retaining the capacity to differentiate into a host of functionally distinct cell types. In addition, these cells could be potentially used as therapeutic agents in regenerative medicine. Differentiation of hESCs involves selective activation or silencing of genes, a process controlled in part by the epigenetic state of the cell. In order to gain a better understanding of the epigenetic mechanisms regulating differentiation of hESCs, and produce general reference epigenome maps of the human cells, we propose to establish an Epigenome Center in San Diego. Our center will be focused on both undifferentiated hESC and four hESC-derived early embryonic cell lineages including extraembryonic endoderm, trophoblast, mesendoderm (a common precursor to mesodermal and endodermal lineages), and mesenchymal cells (a specific mesoderm derivative). We have developed and validated high throughput technologies for mapping the state of DNA methylation and chromatin modifications throughout the genome, and will use these methods to generate high-resolution maps of the reference epigenomes. Specifically, we will grow and differentiate hESCs into multiple lineages, and map DNA methylation sites using a newly developed technology that combines bisulfite conversion and whole genome shotgun sequencing. We will also determine the histone modification status in the genome by performing both ChlP-chip and ChlP-Seq analysis. We will develop advanced statistical and algorithmic solutions to facilitate high-throughput sequencing data analysis, and establish an informatics pipeline for collecting, storage, and distribution of epigenome maps. Finally, we will perform integrated data analysis to identify new epigenetic patterns in the genome that could provide insights in mechanisms of epigenetic regulation.
cell type comparison RNA-seq gene expression / transcription Roadmap Epigenomics Project
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Illumina HiSeq 2000
SRP001371

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Input Data

Sample Groups and Experimental Factors


Genome Snapshots

'Genome snapshots' are assorted genomic regions that the creators of this experiment considered of particular interest.

Hoxc Cluster

Hoxb Cluster

Wnt1 Locus

Shh Locus

Main Experimental Results

This is a selection of main results from the data analysis in this experiment. All intermediate results and more data are available from the workflow designer.

Other data generated in this experiment:

Typical analysis workflows my generate dozens or even hundreds of outputs. To condense the amount of information into more easily digestible portions, GeneProf will, by default, only display the experiments input data (here: input data) and a selection of the most important outputs (here: main results). You can drill down into the details of the analysis via the workflow designer or you can display other intermediate outputs here.

Analysis Workflow

This is a schematic representation of the analysis workflow used in this experiment. For more details (parameters, etc.) use the fully-featured workflow designer.
Colours represent types of data (sequences, genomic regions, features, references and files.
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