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RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing

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Published on: August 7, 2021

A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing.

Peng Cui¹, Qiang Lin, Feng Ding

¹The CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100029 Beijing, China.

|August 7, 2010

Summary

Ribosomal RNA depletion RNA-sequencing (rmRNA-seq) detects more intergenic and intronic transcripts than polyA selection RNA-sequencing (mRNA-seq). Different RNA preparations significantly alter gene expression profiles.

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Area of Science:

Transcriptomics
Molecular Biology
Bioinformatics

Background:

RNA sequencing is crucial for understanding gene expression.
Choosing the right RNA preparation method is essential for accurate transcriptomic analysis.
Ribosomal RNA depletion (rmRNA-seq) and polyA selection (mRNA-seq) are common RNA preparation methods.

Purpose of the Study:

To compare the effectiveness of rmRNA-seq and mRNA-seq in capturing diverse RNA species.
To investigate the impact of different RNA preparation methods on gene expression profiles.

Main Methods:

Acquired transcriptomic data from mouse cerebrum using both rmRNA-seq and mRNA-seq.
Analyzed the proportion of uniquely alignable reads in intergenic and intronic regions.
Identified various RNA transcripts, including ncRNAs, snoRNAs, snRNAs, and novel ncRNAs.

Main Results:

rmRNA-seq yielded a higher proportion of reads in intergenic (44%) and intronic (25%) regions compared to mRNA-seq (23% and 15%).
rmRNA-seq identified a broader range of transcripts, including protein-coding genes, ncRNAs, and repeat elements.
Comparative analysis revealed significant variations in gene expression profiles due to different RNA preparations.

Conclusions:

rmRNA-seq is more effective in detecting polyA- or bimorphic transcripts.
RNA sample preparation methods significantly influence transcriptomic data and gene expression profiles.
Researchers should carefully consider RNA preparation methods for accurate and comprehensive transcriptomic studies.