title: EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics.
abstract: BACKGROUND
  Next Generation Sequencing technologies have facilitated differential gene expression analysis through RNA-seq and Tag-seq methods. RNA-seq has biases associated with transcript lengths, lacks uniform coverage of regions in mRNA and requires 10-20 times more reads than a typical Tag-seq. Most existing Tag-seq methods either have biases or not high throughput due to use of restriction enzymes or enzymatic manipulation of 5' ends of mRNA or use of RNA ligations.
  
  
  RESULTS
  We have developed EXpression Profiling through Randomly Sheared cDNA tag Sequencing (EXPRSS) that employs acoustic waves to randomly shear cDNA and generate sequence tags at a relatively defined position (~150-200 bp) from the 3' end of each mRNA. Implementation of the method was verified through comparative analysis of expression data generated from EXPRSS, NlaIII-DGE and Affymetrix microarray and through qPCR quantification of selected genes. EXPRSS is a strand specific and restriction enzyme independent tag sequencing method that does not require cDNA length-based data transformations. EXPRSS is highly reproducible, is high-throughput and it also reveals alternative polyadenylation and polyadenylated antisense transcripts. It is cost-effective using barcoded multiplexing, avoids the biases of existing SAGE and derivative methods and can reveal polyadenylation position from paired-end sequencing.
  
  
  CONCLUSIONS
  EXPRSS Tag-seq provides sensitive and reliable gene expression data and enables high-throughput expression profiling with relatively simple downstream analysis.
authors.forename: Ghanasyam
authors.initials: G
authors.lastname: Rallapalli
authors.forename: Eric M
authors.initials: EM
authors.lastname: Kemen
authors.forename: Alexandre
authors.initials: A
authors.lastname: Robert-Seilaniantz
authors.forename: Cécile
authors.initials: C
authors.lastname: Segonzac
authors.forename: Graham J
authors.initials: GJ
authors.lastname: Etherington
authors.forename: Kee Hoon
authors.initials: KH
authors.lastname: Sohn
authors.forename: Daniel
authors.initials: D
authors.lastname: MacLean
authors.affiliation: The Sainsbury Laboratory, Norwich Research Park, Colney, Norwich, UK NR4 7UH. jonathan.jones@tsl.ac.uk.
authors.forename: Jonathan D G
authors.initials: JD
authors.lastname: Jones
mesh_terms: D020413:3' Untranslated Regions; D017360:Arabidopsis / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D018076:DNA, Complementary / Q000378:metabolism; D015536:Down-Regulation; D020869:Gene Expression Profiling / Q000379:methods*; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing; D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D015854:Up-Regulation
chemical_list: D020413:3' Untranslated Regions; D018076:DNA, Complementary; D012333:RNA, Messenger