Public Resources

Whilst we have a large amount of data generated in the lab, there are also many public resources available for genomic data. These resources can be invaluable for comparative studies, validation of results, and accessing datasets that may not be feasible to generate in-house.

ENCODE Project

ENCODE (Encyclopedia of DNA Elements) is a comprehensive resource that provides a wealth of genomic data, including ChIP-seq, RNA-seq, and DNase-seq datasets across various cell types and conditions. The data is freely available and can be accessed through the ENCODE portal (https://www.encodeproject.org/).

GEO Database

The Gene Expression Omnibus (GEO) is a public repository that archives and freely distributes high-throughput gene expression and other functional genomics datasets. Researchers can search for datasets relevant to their studies and download them for analysis. The GEO database can be accessed at (https://www.ncbi.nlm.nih.gov/geo/).

Often journals will require you to deposit your sequencing data to GEO upon publication, so it is useful to be familiar with this resource. You can see the GEO upload guidance for more information on how to upload data to GEO.

You can also directly upload your data to GEO using their FTP server.

If you navigate to a GEO Series (GSE) page, you can find the FTP link under the “Supplementary files” section. You can copy the FTP link directly into UCSC as a custom track, or use wget or curl to download the files to your local machine or HPC cluster.

It’s important that you know what genome assembly your data is aligned to (e.g., hg19, hg38, mm10) so that you can visualise it correctly in genome browsers like UCSC or IGV.

Searching GEO

GEO is a rich resource, but it can be overwhelming to navigate due to the sheer volume of data available. There is a website called ChIP-Atlas that provides a more user-friendly interface for searching and visualizing ChIP-seq data from GEO. It allows you to filter datasets by species, cell type, and experimental conditions, making it easier to find relevant data. You can export the data found in a tsv format so you can do more refined searches in Excel or R.

However it is a bit glitchy at times, but can be very useful when it works. Just go back to it and try again if you have issues.