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A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells

A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells

Published on: October 28, 2025

Recent developments in StemBase: a tool to study gene expression in human and murine stem cells.

Reatha Sandie¹, Gareth A Palidwor, Matthew R Huska

¹Ottawa Health Research Institute, 501 Smyth Road, Ottawa, ON K1H 8L6, Canada. rsandie@ohri.ca

BMC Research Notes

|March 17, 2009

Summary

StemBase is a growing repository for human and mouse stem cell gene expression data, offering analysis tools to study gene function in stem cell control and differentiation.

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Area of Science:

Bioinformatics
Stem Cell Biology
Genomics

Background:

StemBase was initially developed as a web interface for stem cell gene expression data.
It aimed to facilitate the discovery of gene functions related to stem cell control and differentiation.

Purpose of the Study:

To present StemBase as a comprehensive resource for human and mouse stem cell gene expression data.
To highlight its evolution into a system with advanced data analysis tools.

Main Methods:

Utilizes DNA microarray and Serial Analysis of Gene Expression (SAGE) data.
Provides analysis tools for examining the entire database or specific data subsets.

Main Results:

StemBase has expanded significantly in size and scope.
As of September 1, 2008, it contained gene expression data from 210 stem cell samples across 60 experiments.

Conclusions:

StemBase serves as a valuable tool for studying gene expression in human and murine stem cells.
The resource is publicly accessible at http://www.stembase.ca.