PUBLICATION
High-throughput and quantitative genome-wide messenger RNA sequencing for molecular phenotyping
- Authors
- 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.
- ID
- ZDB-PUB-170214-139
- Date
- 2015
- Source
- BMC Genomics 16: 578 (Journal)
- Registered Authors
- Busch-Nentwich, Elisabeth, Dooley, Christopher, Stemple, Derek L.
- Keywords
- none
- MeSH Terms
-
- Animals
- Computational Biology/methods
- Gene Expression Profiling/methods
- Gene Library
- Genetic Association Studies*/methods
- Genome-Wide Association Study*/methods
- High-Throughput Nucleotide Sequencing*
- Molecular Typing*/methods
- Mutation
- RNA, Messenger/genetics*
- Sequence Analysis, RNA*
- Zebrafish
- PubMed
- 26238335 Full text @ BMC Genomics
Citation
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. 16:578.
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.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping