What can RNA sequencing be used for?

RNA-seq (RNA-sequencing) is a technique that can examine the quantity and sequences of RNA in a sample using next-generation sequencing (NGS). It analyzes the transcriptome, indicating which of the genes encoded in our DNA are turned on or off and to what extent.

Why is RNA-Seq better than qPCR?

Advantages of RNA-Seq vs. qPCR. While qRT-PCR is useful for quantifying the expression of a few genes, it can only detect known sequences. RNA-Seq quantifies individual sequence reads aligned to a reference sequence, producing absolute rather than relative expression values.

What is the most important feature that a reference gene should have?

An ideal reference gene has the following characteristics: first, it is expressed stably in different tissues and cells; second, its expression is not greatly affected by environmental, biological or abiotic stress or other factors; finally, its expression level is similar to that of the target gene.

What type of sequences are used for RNA-seq?

These types include ribosomal RNA (rRNA), transfer RNA (tRNA), long ncRNA (lncRNA; transcripts longer than 200 nucleotides not translated into protein), and many smaller ncRNAs such as microRNA (miRNA). A DNA sequence encoding an ncRNA is often called an “RNA gene”.

Is qPCR more accurate than RNA-seq?

qPCR is much more accurate than a microarray and much more specific than RNAseq. Usually, you will want to verify expression in a specific tissue, growth stage, etc. with all the proper controls and comparisons.

Why should qPCR be used to validate NGS data?

qPCR is still considered the gold standard for gene expression analysis, especially when template copy number is low. In short, NGS provides a great tool for analyzing a large number of genes to narrow down the research interest and qPCR provides a fast, reliable, and cost effective means to verify NGS results.

Why is ChIP-seq important?

ChIP-seq can be used to survey interactions accurately between protein, DNA, and RNA, enabling the interpretation of regulation events central to many biological processes and disease states. Since ChIP-seq provides the actual DNA sequences of the precipitated fragments, the data obtained is of higher resolution.

What is the aim of ChIP?

Chromatin immunoprecipitation, or ChIP, is an antibody-based technology used to selectively enrich specific DNA-binding proteins along with their DNA targets. ChIP is used to investigate a particular protein-DNA interaction, several protein-DNA interactions, or interactions across the whole genome or a subset of genes.

How does Star RNA-Seq work?

STAR uses an uncompressed suffix array (SA) to efficiently search for the MMPs, this allows for quick searching against even the largest reference genomes. Other slower aligners use algorithms that often search for the entire read sequence before splitting reads and performing iterative rounds of mapping.