EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics
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- Title
- EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics
- Authors
- Rallapalli, G; Kemen, EM; Robert-Seilaniantz, A; Segonzac, C; Etherington, GJ; Sohn, KH; MacLean, D; Jones, JDG
- Date Issued
- 2014-05-06
- Publisher
- Springer
- 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 (similar to 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.
- Keywords
- ORIENTED RECOGNITION SITES; RNA-SEQ DATA; GENE-EXPRESSION; HUMAN GENOME; ARABIDOPSIS-THALIANA; ANTISENSE TRANSCRIPTION; DNA CLEAVAGE; MICROARRAY EXPERIMENTS; NUCLEOTIDE-SEQUENCE; MESSENGER-RNA; Next generation sequencing; Tag-seq; High throughput expression profiling; RNA-seq; EXPRSS
- URI
- https://oasis.postech.ac.kr/handle/2014.oak/35766
- DOI
- 10.1186/1471-2164-15-341
- ISSN
- 1471-2164
- Article Type
- Article
- Citation
- BMC GENOMICS, vol. 15, 2014-05-06
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