DC Field | Value | Language |
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dc.contributor.author | Rallapalli, G | - |
dc.contributor.author | Kemen, EM | - |
dc.contributor.author | Robert-Seilaniantz, A | - |
dc.contributor.author | Segonzac, C | - |
dc.contributor.author | Etherington, GJ | - |
dc.contributor.author | Sohn, KH | - |
dc.contributor.author | MacLean, D | - |
dc.contributor.author | Jones, JDG | - |
dc.date.accessioned | 2017-07-19T12:23:39Z | - |
dc.date.available | 2017-07-19T12:23:39Z | - |
dc.date.created | 2016-02-19 | - |
dc.date.issued | 2014-05-06 | - |
dc.identifier.issn | 1471-2164 | - |
dc.identifier.uri | https://oasis.postech.ac.kr/handle/2014.oak/35766 | - |
dc.description.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. | - |
dc.language | English | - |
dc.publisher | Springer | - |
dc.relation.isPartOf | BMC GENOMICS | - |
dc.subject | ORIENTED RECOGNITION SITES | - |
dc.subject | RNA-SEQ DATA | - |
dc.subject | GENE-EXPRESSION | - |
dc.subject | HUMAN GENOME | - |
dc.subject | ARABIDOPSIS-THALIANA | - |
dc.subject | ANTISENSE TRANSCRIPTION | - |
dc.subject | DNA CLEAVAGE | - |
dc.subject | MICROARRAY EXPERIMENTS | - |
dc.subject | NUCLEOTIDE-SEQUENCE | - |
dc.subject | MESSENGER-RNA | - |
dc.subject | Next generation sequencing | - |
dc.subject | Tag-seq | - |
dc.subject | High throughput expression profiling | - |
dc.subject | RNA-seq | - |
dc.subject | EXPRSS | - |
dc.title | EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics | - |
dc.type | Article | - |
dc.identifier.doi | 10.1186/1471-2164-15-341 | - |
dc.type.rims | ART | - |
dc.identifier.bibliographicCitation | BMC GENOMICS, v.15 | - |
dc.identifier.wosid | 000336064200001 | - |
dc.date.tcdate | 2019-03-01 | - |
dc.citation.title | BMC GENOMICS | - |
dc.citation.volume | 15 | - |
dc.contributor.affiliatedAuthor | Sohn, KH | - |
dc.identifier.scopusid | 2-s2.0-84900470899 | - |
dc.description.journalClass | 1 | - |
dc.description.journalClass | 1 | - |
dc.description.wostc | 18 | - |
dc.description.scptc | 16 | * |
dc.date.scptcdate | 2018-05-121 | * |
dc.type.docType | Article | - |
dc.subject.keywordPlus | RNA-SEQ DATA | - |
dc.subject.keywordPlus | GENE-EXPRESSION | - |
dc.subject.keywordPlus | ANTISENSE TRANSCRIPTION | - |
dc.subject.keywordPlus | NUCLEOTIDE-SEQUENCE | - |
dc.subject.keywordPlus | MESSENGER-RNA | - |
dc.subject.keywordPlus | DNA CLEAVAGE | - |
dc.subject.keywordPlus | ARABIDOPSIS | - |
dc.subject.keywordPlus | SAGE | - |
dc.subject.keywordPlus | EFFICIENCY | - |
dc.subject.keywordPlus | LANDSCAPE | - |
dc.subject.keywordAuthor | Next generation sequencing | - |
dc.subject.keywordAuthor | Tag-seq | - |
dc.subject.keywordAuthor | High throughput expression profiling | - |
dc.subject.keywordAuthor | RNA-seq | - |
dc.subject.keywordAuthor | EXPRSS | - |
dc.relation.journalWebOfScienceCategory | Biotechnology & Applied Microbiology | - |
dc.relation.journalWebOfScienceCategory | Genetics & Heredity | - |
dc.description.journalRegisteredClass | scie | - |
dc.description.journalRegisteredClass | scopus | - |
dc.relation.journalResearchArea | Biotechnology & Applied Microbiology | - |
dc.relation.journalResearchArea | Genetics & Heredity | - |
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