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
Abstract
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.
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.
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
Figures
Expression
Phenotype
Mutation and Transgenics
Human Disease / Model Data
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping
Errata and Notes