ArticleBMC genomics2014
EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- DSK2-mediated degradation of F-box protein LAO1 and class I TCPs modulates the nitrogen starvation response.EMBO reports · 2025Article
- Coupling of alternative splicing and alternative polyadenylation.Acta biochimica et biophysica Sinica · 2024Review
- Cell-specific RNA profiling reveals host genes expressed in Arabidopsis cells haustoriated by downy mildew.Plant physiology · 2023Article
- Autophagy modulates the metabolism and growth of tomato fruit during development.Horticulture research · 2022Article
- Oxicam-type non-steroidal anti-inflammatory drugs inhibit NPR1-mediated salicylic acid pathway.Nature communications · 2021Article
- Specific modulation of the root immune system by a community of commensal bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Role ofInternational journal of molecular sciences · 2020Article
- Downy Mildew effector HaRxL21 interacts with the transcriptional repressor TOPLESS to promote pathogen susceptibility.PLoS pathogens · 2020Article
- High-resolution expression profiling of selected gene sets during plant immune activation.Plant biotechnology journal · 2020Article
- Extreme resistance to Potato virus Y in potato carrying the RyPlant biotechnology journal · 2020Article
- Comprehensive functional enrichment analysis of male infertility.Scientific reports · 2017Article
- Alternative Polyadenylation: Methods, Findings, and Impacts.Genomics, proteomics & bioinformatics · 2017Review
- The highly buffered Arabidopsis immune signaling network conceals the functions of its components.PLoS genetics · 2017Article
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- Accelerated cloning of a potato late blight-resistance gene using RenSeq and SMRT sequencing.Nature biotechnology · 2016Article
- Accurate Profiling of Gene Expression and Alternative Polyadenylation with Whole Transcriptome Termini Site Sequencing (WTTS-Seq).Genetics · 2016Article
- Jellyfish Bioactive Compounds: Methods for Wet-Lab Work.Marine drugs · 2016Review
- Multi-level engineering facilitates the production of phenylpropanoid compounds in tomato.Nature communications · 2015Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
backgroundNext 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.
resultsWe 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.
conclusionsEXPRSS Tag-seq provides sensitive and reliable gene expression data and enables high-throughput expression profiling with relatively simple downstream analysis.
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