Introduction
Small RNAs play regulatory roles of downstream genes and modulate chromatin structure of the genome. There are many families of small RNAs being the most widely known microRNAs (miRNAs) and small interfering RNAs (siRNAs). miRNAs play a role in a broad rage of biological process including development, cell differentiation and has been associated with human diseases such as cancer. MicroRNAs can reduce the activity (expression level) of protein coding genes through inhibition of protein translations and destabilisation of the mRNAs via removal of the poly A tail.
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What is small RNAseq?
Small noncoding RNAs act in gene silencing and post-transcriptional regulation of gene expression. Small RNA sequencing (RNA-Seq) is a technique to isolate and sequence small RNA species, such as microRNAs (miRNAs). Small RNA-Seq can query thousands of small RNA and miRNA sequences with unprecedented sensitivity and dynamic range (Source: Illumina).
With small RNA-Seq you can discover novel miRNAs and other small noncoding RNAs, and examine the differential expression of all small RNAs in any sample. You can characterize variations such as isomiRs with single-base resolution, as well as analyze any small RNA or miRNA without prior sequence or secondary structure information (Source: Illumina).
Advantages of Small RNA Sequencing
Generate miRNA sequencing libraries directly from total RNA to understand the role of noncoding RNA.
Understand how post-transcriptional regulation contributes to phenotype
Identify novel biomarkers
Capture the complete range of small RNA and miRNA species
Global community for nextflow Bioinformatics pipelines
nf-core is a community-led project to develop a set of best-practice pipelines built using Nextflow. Pipelines are governed by a set of guidelines, enforced by community code reviews and automatic linting (code testing). A suite of helper tools aim to help people run and develop pipelines.
nf-core small RNAseq pipeline https://nf-co.re/smrnaseq/2.2.3
Let’s now go to hands on excercises: