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=== Early attempts ===
The word "transcriptome" was first used in the 1990s.<ref name="#10022985">{{cite journal | vauthors = Piétu G, Mariage-Samson R, Fayein NA, Matingou C, Eveno E, Houlgatte R, Decraene C, Vandenbrouck Y, Tahi F, Devignes MD, Wirkner U, Ansorge W, Cox D, Nagase T, Nomura N, Auffray C | title = The Genexpress IMAGE knowledge base of the human brain transcriptome: a prototype integrated resource for functional and computational genomics | journal = Genome Research | volume = 9 | issue = 2 | pages = 195–209 | date = February 1999 | pmid = 10022985 | pmc = 310711 | doi=10.1101/gr.9.2.195| doi-broken-date = 2023-12-09 }}</ref><ref name="#9008165">{{cite journal | vauthors = Velculescu VE, Zhang L, Zhou W, Vogelstein J, Basrai MA, Bassett DE, Hieter P, Vogelstein B, Kinzler KW | title = Characterization of the yeast transcriptome | journal = Cell | volume = 88 | issue = 2 | pages = 243–51 | date = January 1997 | pmid = 9008165 | doi = 10.1016/S0092-8674(00)81845-0 | s2cid = 11430660 | doi-access = free }}</ref> In 1995, one of the earliest sequencing-based transcriptomic methods was developed, [[serial analysis of gene expression]] (SAGE), which worked by [[Sanger sequencing]] of concatenated random transcript fragments.<ref name="#7570003">{{cite journal | vauthors = Velculescu VE, Zhang L, Vogelstein B, Kinzler KW | title = Serial analysis of gene expression | journal = Science | volume = 270 | issue = 5235 | pages = 484–7 | date = October 1995 | pmid = 7570003 | doi = 10.1126/science.270.5235.484 | bibcode = 1995Sci...270..484V | s2cid = 16281846 }}</ref> Transcripts were quantified by matching the fragments to known genes. A variant of SAGE using high-throughput sequencing techniques, called digital gene expression analysis, was also briefly used.<ref name="#23290152" /><ref name="#9331369">{{cite journal | vauthors = Audic S, Claverie JM | title = The significance of digital gene expression profiles | journal = Genome Research | volume = 7 | issue = 10 | pages = 986–95 | date = October 1997 | pmid = 9331369 | doi = 10.1101/gr.7.10.986 | doi-access = free }}</ref> However, these methods were largely overtaken by high throughput sequencing of entire transcripts, which provided additional information on transcript structure such as [[alternative splicing|splice variants]].<ref name="#23290152" />
=== Development of contemporary techniques ===
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