The modENCODE project is an international initiative aiming to characterise functional elements in the fly and worm model organisms. To date, they have collected data from over 1800 experiments, including everything from gene expression profiling and copy number variation, to a range of histone modification and transcription factor binding sites.
This is a massively useful community resource – whatever favourite gene or problem you’re working on, it’s likely that due to the wide range of experimental data available, there are modENCODE datasets that could complement your research. This is a quick guide aimed at helping you find out what data exists, and how to get a hold of it.
5 ways of accessing modENCODE data:
1. The faceted data browser
This is my favourite interface for browsing the available datasets. There are a range of filters available for selecting your datasets of interest, and there are links for viewing the data in GBrowse, modMine, and links for downloading it.
This feature exists both on the modENCODE webpage and in modMine. The datasets are sorted into broad categories – for example ‘Chromatin structure’, and each category has a number of studies associated with it – for example ‘Nucleosome mapping’ and ‘Genome-wide chromatin profiling’. Clicking on a study takes you to a list of all the data submissions associated with it.
This feature is available on the front page of modMine, as well as in the top right corner of every modMine page. You can search for your favourite gene, experiment type, PI, etc.
4. FTP download
For easy bulk download of modENCODE data, you can use the FTP interface.
5. On the Amazon cloud
To save you downloading data to a local machine, all of it is available on the Amazon cloud. You can upload your own data too, and do your analysis there. To get started, check out this modENCODE help page.