NCBI Epigenomics
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|---|---|
| Content | |
| Description | epigenomic data sets. |
| Contact | |
| Research center | National Center for Biotechnology Information |
| Authors | Ian M Fingerman |
| Primary citation | Fingerman & al. (2011) |
| Release date | 2010 |
| Access | |
| Website | http://www.ncbi.nlm.nih.gov/epigenomics |
The Epigenomics database at the National Center for Biotechnology Information was a database for whole-genome epigenetics data sets. It was retired on 1 June 2016.
The Epigenomics database of the National Center for Biotechnology Information (NCBI) at the National Institutes of Health (NIH) was launched in June 2010 as a means to collect maps of epigenetic modifications and their occurrence across the human genome. This database provides a publicly available resource for maps in stem cells and primary ex vivo tissues that detail genome-wide landscapes of epigenetic factors that occur in human development and disease.
The primary resources for the content of the Epigenomics Database are derived from two archival databases at the NCBI: The Gene Expression Omnibus (GEO) and the Sequence Read Archive (SRA). The Gene Expression Omnibus is a data system for high-throughput genomic data that is generated from microarray and next-generation sequencing technologies. Data used in the Epigenomics database is a combination of GEO and SRA subsets that are specific to Epigenetic factors. This data is subjected to additional review and organized in a more easily attainable fashion before added to the Epigenomics database.
All of the experiments and corresponding samples in the Epigenomics database are displayed in the default browser. As of October 2013, there are currently 4112 experiments and 1257 samples available in the database. Five studied species are represented in the database, and many data tracks are available including expression of micro and small RNAs, histone modification and histone modifying enzymes, chromatin accessibility and chromatin associated factors, and transcription factors. One such example from the database is a study of certain epigenetic factors in Drosophila melanogaster at the 20- to 24-hour embryonic stage of development.
The Epigenomics database browser contain two fundamental search records, "Experiments" and "Samples".
The Experiment search record refers to one or more experiments with a set of scientific aims. Here a user is able to retrieve full data source information. This information includes the institution of the submitter, links to the original data submissions in GEO and SRA, links to literature citations in PubMed and/or full text articles in Pubmed. Experiment records contain a unique accession number that includes a prefix 'ESS'.
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