Transcriptomics technologies: Difference between revisions

Revision as of 03:40, 24 May 2022

Revision as of 14:16, 24 October 2022

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==History==

[[File:Transcriptomics technique publications over time.svg|thumb|300pxupright=1.4|''Transcriptomics method use over time.'' Published papers referring to RNA-Seq (black), RNA microarray (red), expressed sequence tag (blue), [[differential display|digital differential display]] (green), and serial/cap analysis of gene expression (yellow) since 1990.<ref>{{Cite web|url=http://dan.corlan.net/medline-trend.html|title=Medline trend: automated yearly statistics of PubMed results for any query|website=dan.corlan.net|access-date=2016-10-05}}</ref>]]

Transcriptomics has been characterised by the development of new techniques which have redefined what is possible every decade or so and rendered previous technologies obsolete. The first attempt at capturing a partial human transcriptome was published in 1991 and reported 609 [[Messenger RNA|mRNA]] sequences from the [[human brain]].<ref name="ref2047873"/> In 2008, two human transcriptomes, composed of millions of transcript-derived sequences covering 16,000 genes, were published,<ref name="#18978789">{{cite journal | vauthors = Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ | title = Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing | journal = Nature Genetics | volume = 40 | issue = 12 | pages = 1413–5 | date = December 2008 | pmid = 18978789 | doi = 10.1038/ng.259 | s2cid = 9228930 }}</ref><ref name="#18599741">{{cite journal | vauthors = Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D, Schmidt D, O'Keeffe S, Haas S, Vingron M, Lehrach H, Yaspo ML | display-authors = 6 | title = A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome | journal = Science | volume = 321 | issue = 5891 | pages = 956–60 | date = August 2008 | pmid = 18599741 | doi = 10.1126/science.1160342 | bibcode = 2008Sci...321..956S | s2cid = 10013179 }}</ref> and by 2015 transcriptomes had been published for hundreds of individuals.<ref name="#24037378">{{cite journal | vauthors = Lappalainen T, Sammeth M, Friedländer MR, 't Hoen PA, Monlong J, Rivas MA, Gonzàlez-Porta M, Kurbatova N, Griebel T, Ferreira PG, Barann M, Wieland T, Greger L, van Iterson M, Almlöf J, Ribeca P, Pulyakhina I, Esser D, Giger T, Tikhonov A, Sultan M, Bertier G, MacArthur DG, Lek M, Lizano E, Buermans HP, Padioleau I, Schwarzmayr T, Karlberg O, Ongen H, Kilpinen H, Beltran S, Gut M, Kahlem K, Amstislavskiy V, Stegle O, Pirinen M, Montgomery SB, Donnelly P, McCarthy MI, Flicek P, Strom TM, Lehrach H, Schreiber S, Sudbrak R, Carracedo A, Antonarakis SE, Häsler R, Syvänen AC, van Ommen GJ, Brazma A, Meitinger T, Rosenstiel P, Guigó R, Gut IG, Estivill X, Dermitzakis ET | display-authors = 6 | title = Transcriptome and genome sequencing uncovers functional variation in humans | journal = Nature | volume = 501 | issue = 7468 | pages = 506–11 | date = September 2013 | pmid = 24037378 | pmc = 3918453 | doi = 10.1038/nature12531 | bibcode = 2013Natur.501..506L }}</ref><ref name="#25954002">{{cite journal | vauthors = Melé M, Ferreira PG, Reverter F, DeLuca DS, Monlong J, Sammeth M, Young TR, Goldmann JM, Pervouchine DD, Sullivan TJ, Johnson R, Segrè AV, Djebali S, Niarchou A, Wright FA, Lappalainen T, Calvo M, Getz G, Dermitzakis ET, Ardlie KG, Guigó R | display-authors = 6 | title = Human genomics. The human transcriptome across tissues and individuals | journal = Science | volume = 348 | issue = 6235 | pages = 660–5 | date = May 2015 | pmid = 25954002 | pmc = 4547472 | doi = 10.1126/science.aaa0355 | bibcode = 2015Sci...348..660M }}</ref> Transcriptomes of different [[disease]] states, [[Tissue (biology)|tissues]], or even single [[Cell (biology)|cells]] are now routinely generated.<ref name="#25954002" /><ref name="#24524133">{{cite journal | vauthors = Sandberg R | title = Entering the era of single-cell transcriptomics in biology and medicine | journal = Nature Methods | volume = 11 | issue = 1 | pages = 22–4 | date = January 2014 | pmid = 24524133 | doi = 10.1038/nmeth.2764 | s2cid = 27632439 | url = https://zenodo.org/record/890299 }}</ref><ref name="#26000846">{{cite journal | vauthors = Kolodziejczyk AA, Kim JK, Svensson V, Marioni JC, Teichmann SA | title = The technology and biology of single-cell RNA sequencing | journal = Molecular Cell | volume = 58 | issue = 4 | pages = 610–20 | date = May 2015 | pmid = 26000846 | doi = 10.1016/j.molcel.2015.04.005 | doi-access = free }}</ref> This explosion in transcriptomics has been driven by the rapid development of new technologies with improved sensitivity and economy.<ref name="#23290152">{{cite journal | vauthors = McGettigan PA | title = Transcriptomics in the RNA-seq era | journal = Current Opinion in Chemical Biology | volume = 17 | issue = 1 | pages = 4–11 | date = February 2013 | pmid = 23290152 | doi = 10.1016/j.cbpa.2012.12.008 }}</ref><ref name="#19015660">{{cite journal | vauthors = Wang Z, Gerstein M, Snyder M | title = RNA-Seq: a revolutionary tool for transcriptomics | journal = Nature Reviews Genetics | volume = 10 | issue = 1 | pages = 57–63 | date = January 2009 | pmid = 19015660 | pmc = 2949280 | doi = 10.1038/nrg2484 }}</ref><ref name="#21191423">{{cite journal | vauthors = Ozsolak F, Milos PM | title = RNA sequencing: advances, challenges and opportunities | journal = Nature Reviews Genetics | volume = 12 | issue = 2 | pages = 87–98 | date = February 2011 | pmid = 21191423 | pmc = 3031867 | doi = 10.1038/nrg2934 }}</ref><ref name="#19715439">{{cite journal | vauthors = Morozova O, Hirst M, Marra MA | title = Applications of new sequencing technologies for transcriptome analysis | journal = Annual Review of Genomics and Human Genetics | volume = 10 | pages = 135–51 | date = 2009 | pmid = 19715439 | doi = 10.1146/annurev-genom-082908-145957 }}</ref>