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

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StemMapper: a curated gene expression database for stem cell lineage analysis.

José P Pinto^1,2, Rui S R Machado^1,2, Ramiro Magno^2,3

¹Systems Biology and Bioinformatics Laboratory (SysBioLab), Universidade do Algarve, Faro, 8005-139, Portugal.

Nucleic Acids Research

|October 19, 2017

Summary

This summary is machine-generated.

StemMapper is a new database that simplifies access to stem cell (SC) transcriptomic data. This resource provides curated gene expression data for over 960 transcriptomes, aiding research in aging, development, and diseases.

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Area of Science:

Stem Cell Biology
Genomics
Bioinformatics

Background:

Transcriptomic data is crucial for stem cell (SC) research, impacting fields like aging, development, and disease.
Analyzing the increasing volume of publicly available SC transcriptomic datasets presents significant challenges.

Purpose of the Study:

To introduce StemMapper, a manually curated gene expression database designed to streamline SC research.
To provide a comprehensive and user-friendly resource for accessing and analyzing SC transcriptomic data.

Main Methods:

Integrated transcriptomic datasets from human and mouse SCs.
Implemented rigorous data selection, standardized processing, and quality control for over 960 transcriptomes.
Developed a user-friendly interface for querying, comparing, and visualizing curated gene expression data.

Main Results:

StemMapper offers access to over 960 manually curated transcriptomes covering diverse SC types.
The database features a user-friendly interface for efficient data querying, comparison, and visualization.
A proof-of-principle analysis successfully identified novel astrocyte/neural SC lineage markers.

Conclusions:

StemMapper significantly simplifies access to and analysis of SC transcriptomic data.
This resource has the potential to drive new discoveries and advancements in stem cell biology.
StemMapper is freely accessible online, promoting broader research engagement.