ArticleGenome research2014
Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing.
Article in Genome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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Who cites it
72 citing papers in PubMed.
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- 5'-UTR G-Quadruplex-Mediated Translation Regulation in Eukaryotes: Current Understanding and Methodological Challenges.International journal of molecular sciences · 2025Review
- Selecting differential splicing methods: Practical considerations for short-read RNA sequencing.F1000Research · 2025Review
- Quantifying the regulatory potential of genetic variants via a hybrid sequence-oriented model with SVEN.Nature communications · 2024Article
- Core promoterome of barley embryo.Computational and structural biotechnology journal · 2024Article
- Nanopore guided annotation of transcriptome architectures.mSystems · 2024Article
- Sequence basis of transcription initiation in the human genome.Science (New York, N.Y.) · 2024Article
- Nanopore Guided Annotation of Transcriptome Architectures.bioRxiv : the preprint server for biology · 2024Article
- Long noncoding RNA study: Genome-wide approaches.Genes & diseases · 2023Review
- DNMT and HDAC inhibition induces immunogenic neoantigens from human endogenous retroviral element-derived transcripts.Nature communications · 2023Article
- Dosage compensation of Z sex chromosome genes in avian fibroblast cells.Genome biology · 2023Article
- Current Status of Next-Generation Sequencing in Bone Genetic Diseases.International journal of molecular sciences · 2023Review
- Article
- Linking discoveries, mechanisms, and technologies to develop a clearer perspective on plant long noncoding RNAs.The Plant cell · 2023Review
- CAGE sequencing reveals CFTR-dependent dysregulation of type I IFN signaling in activated cystic fibrosis macrophages.Science advances · 2023Article
- Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes.Nature communications · 2023Article
- SCAFE: a software suite for analysis of transcribed cis-regulatory elements in single cells.Bioinformatics (Oxford, England) · 2022Article
- Article
12 more citing papers are in PubMed but not listed here.
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18 authors.
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No grant is acknowledged in the PubMed record.
Abstract
CAGE (cap analysis gene expression) and RNA-seq are two major technologies used to identify transcript abundances as well as structures. They measure expression by sequencing from either the 5' end of capped molecules (CAGE) or tags randomly distributed along the length of a transcript (RNA-seq). Library protocols for clonally amplified (Illumina, SOLiD, 454 Life Sciences [Roche], Ion Torrent), second-generation sequencing platforms typically employ PCR preamplification prior to clonal amplification, while third-generation, single-molecule sequencers can sequence unamplified libraries. Although these transcriptome profiling platforms have been demonstrated to be individually reproducible, no systematic comparison has been carried out between them. Here we compare CAGE, using both second- and third-generation sequencers, and RNA-seq, using a second-generation sequencer based on a panel of RNA mixtures from two human cell lines to examine power in the discrimination of biological states, detection of differentially expressed genes, linearity of measurements, and quantification reproducibility. We found that the quantified levels of gene expression are largely comparable across platforms and conclude that CAGE and RNA-seq are complementary technologies that can be used to improve incomplete gene models. We also found systematic bias in the second- and third-generation platforms, which is likely due to steps such as linker ligation, cleavage by restriction enzymes, and PCR amplification. This study provides a perspective on the performance of these platforms, which will be a baseline in the design of further experiments to tackle complex transcriptomes uncovered in a wide range of cell types.
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