The variety and volume of data being produced by biological research hold tremendous potential for reuse and drug discovery but are scattered across multiple, disparate sources and lack standardization. Thus, the availability of data does not equate to its easy usability. Researchers and data scientists find it laborious to derive accurate high-quality RNA-seq data from public repositories.
Are you also looking for a one-click solution for RNA-seq data discovery and retrieval? Look no further. This blog discusses Elucidata’s Polly- a biomedical data platform to help you do the same. Polly is a data-centric MLOps platform that provides access to FAIR (Findable, Accessible, Interoperable, and Reusable) multi-omics data from public and proprietary sources.
There are many public-source repositories for high-throughput data on gene expression studies, including those that examine genome methylation, chromatin structure, and genome–protein interactions, and other forms of high-throughput functional genomics data submitted by the research community.
Some of these sources are listed below:
GEO is the most widely used repository for finding RNA-seq data due to the vastness of its data. In this section, we discuss the challenges associated with finding data on GEO and the data itself.
The data on GEO does not follow a particular ontology. So, it might be important to find out the synonyms and the acronyms/ abbreviations of the keyword of interest to improve the search results.
Polly’s OmixAtlas aims to address these issues by ensuring that the metadata from different data types and across different data sources are curated and harmonized.
OmixAtlas is the data warehouse on Polly that provides access to a large number of curated RNA sequencing studies. It is a collection of millions of datasets from public, proprietary, and licensed sources that have been curated, harmonized, and made ready for downstream machine learning and analytical applications. There are essentially 2 different datatypes; Bulk RNA-seq data and Single-cell RNA-seq data grouped under Bulk RNA-seq OmixAtlas and Single-cell OmixAtlas, respectively.
Bulk RNA-seq Omixatlas is a revolutionary technology that enables researchers to analyze gene expression across various cell types and tissues.
Go one step ahead and readily visualize the curated GEO datasets using Phantasus.
Phantasus is a user-friendly web application for interactive gene expression analysis. It simplifies data analysis by offering a seamless approach, from loading, normalizing, and filtering the data to performing differential gene expression and downstream analysis.
The highly curated datasets on Polly allow seamless integration of the Phantasus app, and data can be analyzed readily without the need for preprocessing. Any dataset can be opened on this application on Polly, and a corresponding heatmap will appear.
Polly hosts the world’s largest collection of highly curated, ML-ready bulk and single-cell RNA seq data. Our curation pipelines, high-quality, accurately annotated data, standard workflows, and scientific expertise are used by industries and academia across the globe to accelerate their drug discovery process. Reach out to us to learn more about how to accelerate your research!
Get the latest insights on Biomolecular data and ML