Tag: RNA sequencing

Spatial transcriptomics provide unprecedented access to gene expression information at the location-specific tissue or organ level

October 9, 2021

Nucleic acids-based sequencing techniques such as RNA-seq has revolutionized efforts to obtain differential gene expression patterns of cells. Specifically, time-consuming and expensive DNA microarrays were dominant in the earliest days of differential gene expression analysis. But, the approach has made a comeback in a different format in what is known as spatial transcriptomics. Specifically, spatial … More Spatial transcriptomics provide unprecedented access to gene expression information at the location-specific tissue or organ level

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

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

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

September 4, 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 fragments 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

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

Expert knowledge on pathways and discovery science approaches are dominant problem-solving methodologies in cancer research

December 2, 2019

Advent of sequencing methods that help elucidate the mutational signatures of cancer at the genome level help usher in the use of big data and discovery science approaches in cancer research that have helped identify hitherto unknown pathways and genes as implicated in cancer. Specifically, such DNA sequencing approaches identify mutated genes that could be … More Expert knowledge on pathways and discovery science approaches are dominant problem-solving methodologies in cancer research

Increasing amount of supercomputer time is devoted to data analysis

May 25, 2019

Supercomputers are typically used for data intensive and computationally expensive complex simulations in the geosciences, structural biology, meteorology and cosmology. But, increasingly, supercomputers are used for data analysis of large datasets in myriad fields such as astronomy, genomics, and proteomics. More importantly, the advent of machine learning and the desire to find otherwise hidden patterns … More Increasing amount of supercomputer time is devoted to data analysis