Tag: differential gene expression

Quantitative PCR could help validate the results of RNA-seq

September 5, 2021

RNA-sequencing (RNA-seq) is the current dominant technique for profiling differential gene expression. Being a comprehensive technique, RNA-seq could profile the expression levels of all genes in a genome in an unbiased manner. But, is there an alternative or complementary technique whose data could help corroborate the findings from RNA-seq? The answer is yes, and the … More Quantitative PCR could help validate the results of RNA-seq

Relative lack of RNA material may impact on the quality of single cell RNA sequencing results

August 14, 2021

RNA-sequencing derives its RNA material for analysis from an ensemble of at least thousands to millions of cells. Hence, it is an aggregate technique that could not observe single cell level heterogeneity in the cell population. This necessarily meant that population level RNA-seq could not answer questions pertaining to how different cells contribute to population … More Relative lack of RNA material may impact on the quality of single cell RNA sequencing results

Utility of single cell RNA-sequencing depends on the biological question asked

April 20, 2021

Understanding differential gene expression at the single cell level offers a unique view into cellular transcriptional dynamics as well as stochasticity of gene expression at the population level. Single cell RNA-sequencing has emerged as the de facto tool for understanding differential gene expression in cells. However, when should we probe differential gene expression at the … More Utility of single cell RNA-sequencing depends on the biological question asked

Profiling gene expression: RNA-seq offers a broader approach compared to DNA microarray

March 12, 2021

Although genomic information contains all the instructions for manufacturing a protein, genes could be silent and not expressed. Thus, gene expression is a critical measure of the state of a gene as well as its relation to the phenotype of a cell. But, what is more important is the relative expression levels of different genes … More Profiling gene expression: RNA-seq offers a broader approach compared to DNA microarray

RNA-seq transcriptome data frequently requires high performance computing for data analysis

March 3, 2021

Analysis of differential gene expression in strains exposed to different conditions have, in the contemporary era, been undertaken by two key technologies: RNA sequencing or microarray analysis. Between the two, RNA sequencing is increasingly dominant due to a combination of availability of commercial kits for RNA extraction and library preparation, as well as lower cost … More RNA-seq transcriptome data frequently requires high performance computing for data analysis

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

Next-generation sequencing of short reads usually incur errors at both ends of the read

October 23, 2020

RNA sequencing of coding genes has emerged as the dominant technology for profiling differential gene expression in a variety of cells. Enabling this revolution in biological research is next-generation short read sequencing. Using proprietary technologies in different formats, RNA extracted from cells are first processed to allow high throughput sequencing of short reads. One important … More Next-generation sequencing of short reads usually incur errors at both ends of the read

Large numbers of reads are needed to profile low expression genes in RNA-seq

July 10, 2020

RNA sequencing has emerged as the dominant technique for profiling differential gene expression in cells and tissues. In this approach, RNA is first reverse transcribed to form complementary DNA (cDNA), which is subsequently digested to generate short fragment for high throughput sequencing. Essentially, the technique sequence DNA, not RNA. Due to the short reads, hundreds … More Large numbers of reads are needed to profile low expression genes in RNA-seq

Difficulty in defining a reference human proteome

May 6, 2020

Compared to genomics, proteomics is less data rich and ill-defined. This largely stems from the phenomenon of differential gene expression and protein production arising from different growth phases or nutritional and environmental conditions. Hence, it is theoretically difficult to define a reference human proteome, since a given proteome is only associated with a particular set … More Difficulty in defining a reference human proteome