High-throughput and quantitative genome-wide messenger RNA sequencing for molecular phenotyping

John E. Collins; Neha Wali; Ian M. Sealy; James A. Morris; Richard J. White; Steven R. Leonard; David K. Jackson; Matthew C. Jones; Nathalie C. Smerdon; Jorge Zamora; Christopher M. Dooley; Samantha N. Carruthers; Jeffrey C. Barrett; Derek L. Stemple; Elisabeth M. Busch-Nentwich

doi:10.1186/s12864-015-1788-6

High-throughput and quantitative genome-wide messenger RNA sequencing for molecular phenotyping

John E. Collins, Neha Wali, Ian M. Sealy, James A. Morris, Richard J. White, Steven R. Leonard, David K. Jackson, Matthew C. Jones, Nathalie C. Smerdon, Jorge Zamora, Christopher M. Dooley, Samantha N. Carruthers, Jeffrey C. Barrett, Derek L. Stemple^*, Elisabeth M. Busch-Nentwich

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

14 Citations (Scopus)

Abstract

Background: We present a genome-wide messenger RNA (mRNA) sequencing technique that converts small amounts of RNA from many samples into molecular phenotypes. It encompasses all steps from sample preparation to sequence analysis and is applicable to baseline profiling or perturbation measurements. Results: Multiplex sequencing of transcript 3' ends identifies differential transcript abundance independent of gene annotation. We show that increasing biological replicate number while maintaining the total amount of sequencing identifies more differentially abundant transcripts. Conclusions: This method can be implemented on polyadenylated RNA from any organism with an annotated reference genome and in any laboratory with access to Illumina sequencing.

Original language	English
Article number	578
Journal	BMC Genomics
Volume	16
Issue number	1
DOIs	https://doi.org/10.1186/s12864-015-1788-6
Publication status	Published - 5 Aug 2015
Externally published	Yes

Bibliographical note

Publisher Copyright:
© 2015 Collins et al.

Keywords

Molecular phenotype
RNA-seq
mRNA transcript profiling

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10.1186/s12864-015-1788-6

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Collins, J. E., Wali, N., Sealy, I. M., Morris, J. A., White, R. J., Leonard, S. R., Jackson, D. K., Jones, M. C., Smerdon, N. C., Zamora, J., Dooley, C. M., Carruthers, S. N., Barrett, J. C., Stemple, D. L., & Busch-Nentwich, E. M. (2015). High-throughput and quantitative genome-wide messenger RNA sequencing for molecular phenotyping. BMC Genomics, 16(1), Article 578. https://doi.org/10.1186/s12864-015-1788-6

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title = "High-throughput and quantitative genome-wide messenger RNA sequencing for molecular phenotyping",

abstract = "Background: We present a genome-wide messenger RNA (mRNA) sequencing technique that converts small amounts of RNA from many samples into molecular phenotypes. It encompasses all steps from sample preparation to sequence analysis and is applicable to baseline profiling or perturbation measurements. Results: Multiplex sequencing of transcript 3' ends identifies differential transcript abundance independent of gene annotation. We show that increasing biological replicate number while maintaining the total amount of sequencing identifies more differentially abundant transcripts. Conclusions: This method can be implemented on polyadenylated RNA from any organism with an annotated reference genome and in any laboratory with access to Illumina sequencing.",

keywords = "Molecular phenotype, RNA-seq, mRNA transcript profiling",

author = "Collins, {John E.} and Neha Wali and Sealy, {Ian M.} and Morris, {James A.} and White, {Richard J.} and Leonard, {Steven R.} and Jackson, {David K.} and Jones, {Matthew C.} and Smerdon, {Nathalie C.} and Jorge Zamora and Dooley, {Christopher M.} and Carruthers, {Samantha N.} and Barrett, {Jeffrey C.} and Stemple, {Derek L.} and Busch-Nentwich, {Elisabeth M.}",

note = "Publisher Copyright: {\textcopyright} 2015 Collins et al.",

year = "2015",

month = aug,

day = "5",

doi = "10.1186/s12864-015-1788-6",

language = "English",

volume = "16",

journal = "BMC Genomics",

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Collins, JE, Wali, N, Sealy, IM, Morris, JA, White, RJ, Leonard, SR, Jackson, DK, Jones, MC, Smerdon, NC, Zamora, J, Dooley, CM, Carruthers, SN, Barrett, JC, Stemple, DL & Busch-Nentwich, EM 2015, 'High-throughput and quantitative genome-wide messenger RNA sequencing for molecular phenotyping', BMC Genomics, vol. 16, no. 1, 578. https://doi.org/10.1186/s12864-015-1788-6

TY - JOUR

T1 - High-throughput and quantitative genome-wide messenger RNA sequencing for molecular phenotyping

AU - Collins, John E.

AU - Wali, Neha

AU - Sealy, Ian M.

AU - Morris, James A.

AU - White, Richard J.

AU - Leonard, Steven R.

AU - Jackson, David K.

AU - Jones, Matthew C.

AU - Smerdon, Nathalie C.

AU - Zamora, Jorge

AU - Dooley, Christopher M.

AU - Carruthers, Samantha N.

AU - Barrett, Jeffrey C.

AU - Stemple, Derek L.

AU - Busch-Nentwich, Elisabeth M.

PY - 2015/8/5

Y1 - 2015/8/5

N2 - Background: We present a genome-wide messenger RNA (mRNA) sequencing technique that converts small amounts of RNA from many samples into molecular phenotypes. It encompasses all steps from sample preparation to sequence analysis and is applicable to baseline profiling or perturbation measurements. Results: Multiplex sequencing of transcript 3' ends identifies differential transcript abundance independent of gene annotation. We show that increasing biological replicate number while maintaining the total amount of sequencing identifies more differentially abundant transcripts. Conclusions: This method can be implemented on polyadenylated RNA from any organism with an annotated reference genome and in any laboratory with access to Illumina sequencing.

AB - Background: We present a genome-wide messenger RNA (mRNA) sequencing technique that converts small amounts of RNA from many samples into molecular phenotypes. It encompasses all steps from sample preparation to sequence analysis and is applicable to baseline profiling or perturbation measurements. Results: Multiplex sequencing of transcript 3' ends identifies differential transcript abundance independent of gene annotation. We show that increasing biological replicate number while maintaining the total amount of sequencing identifies more differentially abundant transcripts. Conclusions: This method can be implemented on polyadenylated RNA from any organism with an annotated reference genome and in any laboratory with access to Illumina sequencing.

KW - Molecular phenotype

KW - RNA-seq

KW - mRNA transcript profiling

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U2 - 10.1186/s12864-015-1788-6

DO - 10.1186/s12864-015-1788-6

M3 - Article

C2 - 26238335

AN - SCOPUS:84938586261

SN - 1471-2164

VL - 16

JO - BMC Genomics

JF - BMC Genomics

IS - 1

M1 - 578

ER -

High-throughput and quantitative genome-wide messenger RNA sequencing for molecular phenotyping

Abstract

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Keywords

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