Bacterial mRNA sequencing through targeted rRNA depletion for efficient RNA-seq in varied species and co-cultures
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ABSTRACT:
PROVIDER: PRJNA925939 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23173800_1.fastq.gz | Fastqsanger.gz | |||
| SRR23173800_2.fastq.gz | Fastqsanger.gz | |||
| SRR23173801_1.fastq.gz | Fastqsanger.gz | |||
| SRR23173801_2.fastq.gz | Fastqsanger.gz | |||
| SRR23173802_1.fastq.gz | Fastqsanger.gz |
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Project description:ImportanceMicrobes present one of the most diverse sources of biochemistry in nature, and mRNA sequencing provides a comprehensive view of this biological activity by quantitatively measuring microbial transcriptomes. However, efficient mRNA capture for sequencing presents significant challenges in prokaryotes as mRNAs are not poly-adenylated and typically make up less than 5% of total RNA compared with rRNAs that exceed 80%. Recently developed methods for sequencing bacterial mRNA typically rely on depleting rRNA by tiling large probe sets against rRNAs; however, such approaches are expensive, time-consuming, and challenging to scale to varied bacterial species and complex microbial communities. Therefore, we developed EMBR-seq+, a method that requires fewer than 10 short oligonucleotides per rRNA to achieve up to 99% rRNA depletion in diverse bacterial species. Finally, EMBR-seq+ resulted in a deeper view of the transcriptome, enabling systematic quantification of how microbial interactions result in altering the transcriptional state of bacteria within co-cultures.
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