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Microarray and sequencing flow cell. Microarrays and RNA-seq rely on image analysis in different ways. In a microarray chip, each spot on a chip is a defined oligonucleotide probe, and fluorescence intensity directly detects the abundance of a specific sequence (Affymetrix).
RNA-seq is emerging (2013) as the method of choice for measuring transcriptomes of organisms, though the older technique of DNA microarrays is still used. [1] RNA-seq measures the transcription of a specific gene by converting long RNAs into a library of cDNA fragments. The cDNA fragments are then sequenced using high-throughput sequencing ...
RNA-Seq (named as an abbreviation of RNA sequencing) is a technique that uses next-generation sequencing to reveal the presence and quantity of RNA molecules in a biological sample, providing a snapshot of gene expression in the sample, also known as transcriptome.
RNA Seq Experiment. The single-cell RNA-seq technique converts a population of RNAs to a library of cDNA fragments. These fragments are sequenced by high-throughput next generation sequencing techniques and the reads are mapped back to the reference genome, providing a count of the number of reads associated with each gene. [13]
RIP-seq: Involves sequencing the RNAs that were pulled down using high-throughput sequencing rather than analyzing them with a microarray. [5] Authors Zhao et al., 2010. [ 10 ] combined the RNA immunoprecipitation procedure with RNA sequencing .
However, SAGE sampling is based on sequencing mRNA output, not on hybridization of mRNA output to probes, so transcription levels are measured more quantitatively than by microarray. In addition, the mRNA sequences do not need to be known a priori , so genes or gene variants which are not known can be discovered.
Example of an approximately 40,000 probe spotted oligo microarray with enlarged inset to show detail. Microarray analysis techniques are used in interpreting the data generated from experiments on DNA (Gene chip analysis), RNA, and protein microarrays, which allow researchers to investigate the expression state of a large number of genes – in many cases, an organism's entire genome – in a ...
Whereas high sequence coverage for a genome may indicate the presence of repetitive sequences (and thus be masked), for a transcriptome, they may indicate abundance. In addition, unlike genome sequencing, transcriptome sequencing can be strand-specific, due to the possibility of both sense and antisense transcripts. Finally, it can be difficult ...