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<p><span style="font-size:14px">Transcriptomics is the study of the transcriptome - the all set of RNA transcripts which are produced under specific circumstances in one cell or population of cells - using high throughout methods such as microarray analysis.</span></p>
<p><span style="font-size:14px"><u>## Analysis ##</u></span></p>
<p><span style="font-size:14px">A number of organism-specific transcriptome databases have been constructed and annotated to aid in the identification of genes that are differentially expressed in distinct cell populations. RNA-Seq is emerging as the method of choice for measuring transcriptomes of organisms, though the older technique of DNA microarrays is still used.</span></p>
<p><span style="font-size:14px">1) <strong>RNA-Seq</strong></span></p>
<p><span style="font-size:14px">RNA-seq (RNA sequencing), also called whole transcriptome shotgun sequencing<span style="line-height:17.3333px">, </span>uses next-generation sequencing to reveal the presence and quantity of RNA in a biological sample at a given moment in time. RNA-Seq is used to analyze the continually changing cellular transcriptome. Specifically, RNA-Seq facilitates the ability to look at alternative gene spliced transcripts, post-transcriptional modifications, gene fusion, mutations, SNPs and changes in gene expression.<span style="line-height:17.3333px"> </span>In addition to mRNA transcripts, RNA-Seq can look at different populations of RNA to include total RNA, small RNA, such as miRNA, tRNA and ribosomal profiling. RNA-Seq can also be used to determine exon/intron boundaries and verify or amend previously annotated 5’ and 3’ gene boundaries. Prior to RNA-Seq, gene expression studies were done with hybridization-based microarrays. Issues with microarrays include cross-hybridization artifacts, poor quantification of lowly and highly expressed genes, and the knowledge of the sequence.<span style="line-height:17.3333px"> </span>Because of these technical issues, transcriptomics transitioned to sequencing-based methods. These progressed from Sanger sequencing of Expressed Sequence Tag libraries, to chemical tag-based methods and finally to the current technology, NGS of cDNA. </span></p>
<p><span style="font-size:14px">2)<strong> DNA microarray</strong></span></p>
<p><span style="font-size:14px">A DNA microarray is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome. Each DNA spot contains picomoles of a specific DNA sequence, known as proves. These can be a short section of a gene or other DNA element that are used to hybridize a cDNA or cRNA (also called anti-sense RNA) sample under high-stringency conditions. Probe-target hybridization is usually detected and quantified by detection of fluorophore-, silver-, or chemiluminescence-labeled targets to determine relative abundance of nucleic acid sequences in the target.</span></p>
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