Tag: RNA-seq

Gene expression studies inform us of the underlying mechanisms that give rise to an observed phenotype

April 18, 2024

In recent years, gene expression studies have moved into an essential item in many biological studies. Such determination of gene expression pattern could occur at the mRNA or protein level, and helps us understand the molecular underpinnings of certain phenotype at the macroscale. For example, in Escherichia coli cultivated under anaerobic conditions, there is likely … More Gene expression studies inform us of the underlying mechanisms that give rise to an observed phenotype

RNA-seq is a label-free, unbiased genome scale transcriptome profiling technique

March 21, 2024

Understanding gene expression pattern of cells in different health and disease conditions have evolved from an academic curiosity 20 years ago into an almost essential aspect of many biological research workflows. The reason is our newfound ability at correlating gene expression pattern with cellular behaviour and phenotype. To this end, one technique stands out amongst … More RNA-seq is a label-free, unbiased genome scale transcriptome profiling technique

Reference genome provides genomic loci to align the sequence reads from RNA-seq experiments

February 20, 2024

RNA-seq is a popular and accessible transcriptome profiling method that is increasingly used in biological sciences and medical research. It provides a genome scale unbiased view of the gene expression pattern of the cells and tissues, that help provides a mechanistic perspective to phenotypic behaviour and morphological changes. To analyse such an expansive sequence read … More Reference genome provides genomic loci to align the sequence reads from RNA-seq experiments

Hard to find RNA-seq raw dataset for human diseased cells and tissues

December 10, 2023

Understanding the gene expression pattern of diseased human cells and tissues will provide needed guidance for developing suitable treatment plans for patients. It is with this notion in mind that I set out to search for RNA-seq raw dataset for diseased human cells and tissues on public databases. But, the search is futile as many … More Hard to find RNA-seq raw dataset for human diseased cells and tissues

Difficulty in finding RNA-seq raw dataset for profiling microbes in human tissue samples

December 10, 2023

Over the past 10 years, it has been gradually accepted by the scientific community that there exists a consortium of microbes in association with many human organs such as the gastrointestinal tract and skin. Hence, I thought of searching for publicly available RNA-seq raw dataset from GenBank and European Nucleotide Archive to provide raw data … More Difficulty in finding RNA-seq raw dataset for profiling microbes in human tissue samples

Use of RNA-seq to identify expressed genes in a newly sequenced genome

November 5, 2023

RNA-seq is commonly used to decipher the gene expression pattern of different species in an organism or for profiling different cancer subtypes in a cancer model system. However, the approach can also be used to identify expressed genes in a newly sequenced genome. For example, in biological sciences, there are ample opportunities to work with … More Use of RNA-seq to identify expressed genes in a newly sequenced genome

Future trend in RNA sequencing will likely see the rise of longer read sequencing as well as higher adoption of single cell RNA sequencing

December 12, 2022

RNA sequencing (or RNA-seq) is the dominant approach for gene expression analysis in the contemporary era. However, the approach is still not widely adopted given the huge demand on computational resources for data analysis, as well as the high cost of using next-generation sequencing to process millions or tens of millions of reads. Currently, the … More Future trend in RNA sequencing will likely see the rise of longer read sequencing as well as higher adoption of single cell RNA sequencing

RNA-seq is moving towards long-read sequencing of mRNA transcripts

April 15, 2022

Together with DNA microarray, RNA-seq is the dominant approach for profiling gene expression in a variety of cell types and species. Aided by the advent of short read next-generation sequencing, complete workflows with instrumented approaches and data analysis pipelines have been developed for RNA-seq. Known as short-read sequencing RNA-seq, these approaches have far-reaching impacts on … More RNA-seq is moving towards long-read sequencing of mRNA transcripts

Spatially-resolved single cell RNA-seq would provide unprecedented access to differential gene expression at the sub-tissue level

February 26, 2021

Neighbouring cells or cell clusters of a tissue likely have differentiated functions even as they cooperate at the aggregate level to maintain organ function. However, up-to-now such spatially-resolved differential gene expression has been difficult to probe as current methods for interrogating gene expression at the single cell level destroys spatial information embedded within the tissue … More Spatially-resolved single cell RNA-seq would provide unprecedented access to differential gene expression at the sub-tissue level

Ribosome profiling surveys the complement of mRNA undergoing active translation

December 25, 2020

Differential gene expression is one highly coordinated ancestral mechanism that allow cells to respond to new environmental and nutritional status while conserving cellular resources for use when necessary. Such an approach enables cells to only express the genes needed at a particular moment; thereby, reducing wastage of cellular energy and building blocks that would be … More Ribosome profiling surveys the complement of mRNA undergoing active translation