RNA-seq — wikipedia

RNA-seq (RNA sequenc­ing), also called whole tran­scrip­tome shot­gun sequencing(WTSS), uses next-gen­er­a­tion sequenc­ing (NGS) 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. 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. 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 (e.g., seri­al analy­sis of gene expres­sion), and final­ly to the cur­rent tech­nol­o­gy, NGS of cDNA (notably RNA-Seq).

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