Related Experiment Video
Updated: Mar 11, 2026
10:10
Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2
Published on: September 18, 2021
42.3K
The Lair: a resource for exploratory analysis of published RNA-Seq data
Harold Pimentel1, Pascal Sturmfels2, Nicolas Bray3
1Department of Computer Science, University of California, Berkeley, 387 Soda Hall, Berkeley, 94720, USA.
BMC Bioinformatics
|December 2, 2016
Summary
Researchers developed new tools to easily analyze RNA sequencing (RNA-Seq) data from public archives, improving research reproducibility. This makes complex genomic data accessible for exploring published findings without needing specialized bioinformatics skills.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Growing demand for research reproducibility necessitates accessible archiving of sequencing data.
- Existing archived sequencing data is often challenging to utilize for reproducing published results.
- Large-scale archiving of sequencing data is crucial for scientific integrity.
Purpose of the Study:
- To develop a user-friendly system for processing and analyzing RNA sequencing (RNA-Seq) data.
- To create an easily extendable resource for analyzing data underlying published research papers.
- To make exploration of archived genomic data accessible to researchers without technical expertise.
Main Methods:
- Development of a series of tools for RNA-Seq data processing and analysis.
- Integration of tools with the Sequence Read Archive (SRA).
- Creation of a database and associated tools for data exploration.
Main Results:
- Established an easily extendable resource for analyzing published research data.
- Enabled accessible and usable exploration of archived RNA-Seq data.
- Facilitated data analysis for researchers lacking specialized bioinformatics skills.
Conclusions:
- The developed system enhances the practical utility of archived sequencing data.
- Increased accessibility of RNA-Seq data analysis promotes research reproducibility.
- The Lair provides a valuable resource for the scientific community.
Related Concept Videos
03:21RNA-seq
12.3K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
12.3K
02:24Ribosome Profiling
4.3K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
4.3K