Microarrays versus RNA-seq· What are the maindifferences between the two techniques?Several distictions exist between microarrays andRNA-seq, especially when when each is appropriate and general usage. First,microarray tends to be used in genomics, epigenomics, transcriptomes, and proteomicsstudies. We see RNA-seq utilized typically in transcriptomes studies. The microarray technique was the very firstused in doing a global analysis visualizing mRNA changes. With microarrays, floursecentdyes are used to label targets which are incorporated with the gene chip.
Thetarget that was incubated with the gene chip but not attached is then washed off,and the chip is lasered to scan for any hybridization events. Today, whole genomes are printed on the genechips, as opposed to the original chips which could only hold relatively long portionsof sequences. Results between the studies are similar in general, but RNA-seqhas a higher sensitivity then microarrays. Moreover, in RNA-seq, you don’t haveto have the genome sequenced which is a massive constraint with a microarray insome circumstances.Unlike microarray, RNA-seq is not based on thehybridization events to a gene chip, but rather in sequencing directly. Withthis method the RNA is extracted and fragmented to bp sizes ranging from200-400. These fragments are copied to reveal cDNA.
Once cDNA is present, it issequenced similarly to any high-throughput sequencing method. All the reads arethen mapped alongside the genome, and the amount of mapped sequences will givean indication of the abundance of that transcript in one’s sample. · If you are workingwith a model organism, which is/are the main advantage of Microarray technologyover RNAseq?· One may elect to usemicroarray over RNAseq because of the competitive nature of signals from genesor transcripts.
For example, when performing an independent component analysis,the innate competitiveness of signals from the samples may muck up the results ofan RNA-seq analysis, making microarray advantageous in this type of situation· Microarrays can capturesome time moments of a predefined gene set, whereas RNAseq would not show justthe subset, but the entire genome. Depending on what’s needed this could makemicroarray more advantageous.· Microarray are highlyvariable in their usage, from transcriptomes to epigenomes and even proteomes.RNAseqs are typically only of significant use when studying transcriptomes · Which kind of genesare better studied/discovered with RNAseq?Genes from transcriptomes are best studiedusing RNA-seq