The developmental transcriptome of Drosophila melanogaster

Brenton R. Graveley; Angela N. Brooks; Joseph W. Carlson; Michael O. Duff; Jane M. Landolin; Li Yang; Carlo G. Artieri; Marijke J. Van Baren; Nathan Boley; Benjamin W. Booth; James B. Brown; Lucy Cherbas; Carrie A. Davis; Alex Dobin; Renhua Li; Wei Lin; John H. Malone; Nicolas R. Mattiuzzo; David Miller; David Sturgill; Brian B. Tuch; Chris Zaleski; Dayu Zhang; Marco Blanchette; Sandrine Dudoit; Brian Eads; Richard E. Green; Ann Hammonds; Lichun Jiang; Phil Kapranov; Laura Langton; Norbert Perrimon; Jeremy E. Sandler; Kenneth H. Wan; Aarron Willingham; Yu Zhang; Yi Zou; Justen Andrews; Peter J. Bickel; Steven E. Brenner; Michael R. Brent; Peter Cherbas; Thomas R. Gingeras; Roger A. Hoskins; Thomas C. Kaufman; Brian Oliver; Susan E. Celniker

doi:10.1038/nature09715

The developmental transcriptome of Drosophila melanogaster

Brenton R. Graveley, Angela N. Brooks, Joseph W. Carlson, Michael O. Duff, Jane M. Landolin, Li Yang, Carlo G. Artieri, Marijke J. Van Baren, Nathan Boley, Benjamin W. Booth, James B. Brown, Lucy Cherbas, Carrie A. Davis, Alex Dobin, Renhua Li, Wei Lin, John H. Malone, Nicolas R. Mattiuzzo, David Miller, David SturgillBrian B. Tuch, Chris Zaleski, Dayu Zhang, Marco Blanchette, Sandrine Dudoit, Brian Eads, Richard E. Green, Ann Hammonds, Lichun Jiang, Phil Kapranov, Laura Langton, Norbert Perrimon, Jeremy E. Sandler, Kenneth H. Wan, Aarron Willingham, Yu Zhang, Yi Zou, Justen Andrews, Peter J. Bickel, Steven E. Brenner, Michael R. Brent, Peter Cherbas, Thomas R. Gingeras, Roger A. Hoskins, Thomas C. Kaufman, Brian Oliver, Susan E. Celniker

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Abstract

Drosophila melanogaster is one of the most well studied genetic model organisms; nonetheless, its genome still contains unannotated coding and non-coding genes, transcripts, exons and RNA editing sites. Full discovery and annotation are pre-requisites for understanding how the regulation of transcription, splicing and RNA editing directs the development of this complex organism. Here we used RNA-Seq, tiling microarrays and cDNA sequencing to explore the transcriptome in 30 distinct developmental stages. We identified 111,195 new elements, including thousands of genes, coding and non-coding transcripts, exons, splicing and editing events, and inferred protein isoforms that previously eluded discovery using established experimental, prediction and conservation-based approaches. These data substantially expand the number of known transcribed elements in the Drosophila genome and provide a high-resolution view of transcriptome dynamics throughout development.

Original language	English
Pages (from-to)	473-479
Number of pages	7
Journal	Nature
Volume	471
Issue number	7339
DOIs	https://doi.org/10.1038/nature09715
State	Published - 24 Mar 2011
Externally published	Yes

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10.1038/nature09715

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Graveley, B. R., Brooks, A. N., Carlson, J. W., Duff, M. O., Landolin, J. M., Yang, L., Artieri, C. G., Van Baren, M. J., Boley, N., Booth, B. W., Brown, J. B., Cherbas, L., Davis, C. A., Dobin, A., Li, R., Lin, W., Malone, J. H., Mattiuzzo, N. R., Miller, D., ... Celniker, S. E. (2011). The developmental transcriptome of Drosophila melanogaster. Nature, 471(7339), 473-479. https://doi.org/10.1038/nature09715

@article{dc931fd5aa534deab7826c50859761b8,

title = "The developmental transcriptome of Drosophila melanogaster",

abstract = "Drosophila melanogaster is one of the most well studied genetic model organisms; nonetheless, its genome still contains unannotated coding and non-coding genes, transcripts, exons and RNA editing sites. Full discovery and annotation are pre-requisites for understanding how the regulation of transcription, splicing and RNA editing directs the development of this complex organism. Here we used RNA-Seq, tiling microarrays and cDNA sequencing to explore the transcriptome in 30 distinct developmental stages. We identified 111,195 new elements, including thousands of genes, coding and non-coding transcripts, exons, splicing and editing events, and inferred protein isoforms that previously eluded discovery using established experimental, prediction and conservation-based approaches. These data substantially expand the number of known transcribed elements in the Drosophila genome and provide a high-resolution view of transcriptome dynamics throughout development.",

author = "Graveley, {Brenton R.} and Brooks, {Angela N.} and Carlson, {Joseph W.} and Duff, {Michael O.} and Landolin, {Jane M.} and Li Yang and Artieri, {Carlo G.} and {Van Baren}, {Marijke J.} and Nathan Boley and Booth, {Benjamin W.} and Brown, {James B.} and Lucy Cherbas and Davis, {Carrie A.} and Alex Dobin and Renhua Li and Wei Lin and Malone, {John H.} and Mattiuzzo, {Nicolas R.} and David Miller and David Sturgill and Tuch, {Brian B.} and Chris Zaleski and Dayu Zhang and Marco Blanchette and Sandrine Dudoit and Brian Eads and Green, {Richard E.} and Ann Hammonds and Lichun Jiang and Phil Kapranov and Laura Langton and Norbert Perrimon and Sandler, {Jeremy E.} and Wan, {Kenneth H.} and Aarron Willingham and Yu Zhang and Yi Zou and Justen Andrews and Bickel, {Peter J.} and Brenner, {Steven E.} and Brent, {Michael R.} and Peter Cherbas and Gingeras, {Thomas R.} and Hoskins, {Roger A.} and Kaufman, {Thomas C.} and Brian Oliver and Celniker, {Susan E.}",

note = "Funding Information: Acknowledgements We thank C. Trapnell and L. Pachter for discussions and assistance with Cufflinks, and E. Clough for comments and feedback. A.N.B. was partially supported by an NSF graduate fellowship. This work was funded by an award from the National Human Genome Research INstitute modENCODE Project (U01 HB004271) to S.E.C. (Principal Investigator) and M.R.B., P.C., T.R.G., B.R.G. and N.P. (co-Principal Investigators) under Department of Energy contract no. DE-AC02-05CH11231, and by the National Institute of Diabetes and Digestive and Kidney Diseases Intramural Research Program (B.O.).",

year = "2011",

month = mar,

day = "24",

doi = "10.1038/nature09715",

language = "English",

volume = "471",

pages = "473--479",

journal = "Nature",

issn = "0028-0836",

number = "7339",

}

Graveley, BR, Brooks, AN, Carlson, JW, Duff, MO, Landolin, JM, Yang, L, Artieri, CG, Van Baren, MJ, Boley, N, Booth, BW, Brown, JB, Cherbas, L, Davis, CA, Dobin, A, Li, R, Lin, W, Malone, JH, Mattiuzzo, NR, Miller, D, Sturgill, D, Tuch, BB, Zaleski, C, Zhang, D, Blanchette, M, Dudoit, S, Eads, B, Green, RE, Hammonds, A, Jiang, L, Kapranov, P, Langton, L, Perrimon, N, Sandler, JE, Wan, KH, Willingham, A, Zhang, Y, Zou, Y, Andrews, J, Bickel, PJ, Brenner, SE, Brent, MR, Cherbas, P, Gingeras, TR, Hoskins, RA, Kaufman, TC, Oliver, B & Celniker, SE 2011, 'The developmental transcriptome of Drosophila melanogaster', Nature, vol. 471, no. 7339, pp. 473-479. https://doi.org/10.1038/nature09715

TY - JOUR

T1 - The developmental transcriptome of Drosophila melanogaster

AU - Graveley, Brenton R.

AU - Brooks, Angela N.

AU - Carlson, Joseph W.

AU - Duff, Michael O.

AU - Landolin, Jane M.

AU - Yang, Li

AU - Artieri, Carlo G.

AU - Van Baren, Marijke J.

AU - Boley, Nathan

AU - Booth, Benjamin W.

AU - Brown, James B.

AU - Cherbas, Lucy

AU - Davis, Carrie A.

AU - Dobin, Alex

AU - Li, Renhua

AU - Lin, Wei

AU - Malone, John H.

AU - Mattiuzzo, Nicolas R.

AU - Miller, David

AU - Sturgill, David

AU - Tuch, Brian B.

AU - Zaleski, Chris

AU - Zhang, Dayu

AU - Blanchette, Marco

AU - Dudoit, Sandrine

AU - Eads, Brian

AU - Green, Richard E.

AU - Hammonds, Ann

AU - Jiang, Lichun

AU - Kapranov, Phil

AU - Langton, Laura

AU - Perrimon, Norbert

AU - Sandler, Jeremy E.

AU - Wan, Kenneth H.

AU - Willingham, Aarron

AU - Zhang, Yu

AU - Zou, Yi

AU - Andrews, Justen

AU - Bickel, Peter J.

AU - Brenner, Steven E.

AU - Brent, Michael R.

AU - Cherbas, Peter

AU - Gingeras, Thomas R.

AU - Hoskins, Roger A.

AU - Kaufman, Thomas C.

AU - Oliver, Brian

AU - Celniker, Susan E.

N1 - Funding Information: Acknowledgements We thank C. Trapnell and L. Pachter for discussions and assistance with Cufflinks, and E. Clough for comments and feedback. A.N.B. was partially supported by an NSF graduate fellowship. This work was funded by an award from the National Human Genome Research INstitute modENCODE Project (U01 HB004271) to S.E.C. (Principal Investigator) and M.R.B., P.C., T.R.G., B.R.G. and N.P. (co-Principal Investigators) under Department of Energy contract no. DE-AC02-05CH11231, and by the National Institute of Diabetes and Digestive and Kidney Diseases Intramural Research Program (B.O.).

PY - 2011/3/24

Y1 - 2011/3/24

N2 - Drosophila melanogaster is one of the most well studied genetic model organisms; nonetheless, its genome still contains unannotated coding and non-coding genes, transcripts, exons and RNA editing sites. Full discovery and annotation are pre-requisites for understanding how the regulation of transcription, splicing and RNA editing directs the development of this complex organism. Here we used RNA-Seq, tiling microarrays and cDNA sequencing to explore the transcriptome in 30 distinct developmental stages. We identified 111,195 new elements, including thousands of genes, coding and non-coding transcripts, exons, splicing and editing events, and inferred protein isoforms that previously eluded discovery using established experimental, prediction and conservation-based approaches. These data substantially expand the number of known transcribed elements in the Drosophila genome and provide a high-resolution view of transcriptome dynamics throughout development.

AB - Drosophila melanogaster is one of the most well studied genetic model organisms; nonetheless, its genome still contains unannotated coding and non-coding genes, transcripts, exons and RNA editing sites. Full discovery and annotation are pre-requisites for understanding how the regulation of transcription, splicing and RNA editing directs the development of this complex organism. Here we used RNA-Seq, tiling microarrays and cDNA sequencing to explore the transcriptome in 30 distinct developmental stages. We identified 111,195 new elements, including thousands of genes, coding and non-coding transcripts, exons, splicing and editing events, and inferred protein isoforms that previously eluded discovery using established experimental, prediction and conservation-based approaches. These data substantially expand the number of known transcribed elements in the Drosophila genome and provide a high-resolution view of transcriptome dynamics throughout development.

UR - http://www.scopus.com/inward/record.url?scp=79953043801&partnerID=8YFLogxK

U2 - 10.1038/nature09715

DO - 10.1038/nature09715

M3 - Article

C2 - 21179090

AN - SCOPUS:79953043801

SN - 0028-0836

VL - 471

SP - 473

EP - 479

JO - Nature

JF - Nature

IS - 7339

ER -

The developmental transcriptome of Drosophila melanogaster

Abstract

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