ArticleNucleic acids research2010
Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 1 of them a synthesis that pooled it.
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Who cites it
21 citing papers in PubMed, 1 synthesis or guideline pooled it.
- DeepSAGE reveals genetic variants associated with alternative polyadenylation and expression of coding and non-coding transcripts.PLoS genetics · 2013Pooled it
- Widespread 3'UTR capped RNAs derive from G-rich regions in proximity to AGO2 binding sites.BMC biology · 2024Article
- Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq.Genome biology · 2021Article
- Expression of murine muscle-enriched A-type lamin-interacting protein (MLIP) is regulated by tissue-specific alternative transcription start sites.The Journal of biological chemistry · 2018Article
- Comprehensive comparative analysis of 5'-end RNA-sequencing methods.Nature methods · 2018Article
- Undiscovered Physiology of Transcript and Protein Networks.Comprehensive Physiology · 2016Review
- Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium.Nucleic acids research · 2015Article
- NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites.BMC genomics · 2015Article
- Assessing the translational landscape of myogenic differentiation by ribosome profiling.Nucleic acids research · 2015Article
- Remodeling of retrotransposon elements during epigenetic induction of adult visual cortical plasticity by HDAC inhibitors.Epigenetics & chromatin · 2015Article
- Article
- RNA sequencing: from tag-based profiling to resolving complete transcript structure.Cellular and molecular life sciences : CMLS · 2014Review
- Quantitative biology of single neurons.Journal of the Royal Society, Interface · 2012Review
- Deep sequencing of RNA from immune cell-derived vesicles uncovers the selective incorporation of small non-coding RNA biotypes with potential regulatory functions.Nucleic acids research · 2012Article
- Survey of the Applications of NGS to Whole-Genome Sequencing and Expression Profiling.Genomics & informatics · 2012Article
- 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing.Nature protocols · 2012Article
- Automated workflow for preparation of cDNA for cap analysis of gene expression on a single molecule sequencer.PloS one · 2012Article
- Sequencing technologies and genome sequencing.Journal of applied genetics · 2011Review
- Unamplified cap analysis of gene expression on a single-molecule sequencer.Genome research · 2011Article
- Differential gene expression in the siphonophore Nanomia bijuga (Cnidaria) assessed with multiple next-generation sequencing workflows.PloS one · 2011Article
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation sequencing is excellently suited to evaluate the abundance of mRNAs to study gene expression. Here we compare two alternative technologies, cap analysis of gene expression (CAGE) and serial analysis of gene expression (SAGE), for the same RNA samples. Along with quantifying gene expression levels, CAGE can be used to identify tissue-specific transcription start sites, while SAGE monitors 3'-end usage. We used both methods to get more insight into the transcriptional control of myogenesis, studying differential gene expression in differentiated and proliferating C2C12 myoblast cells with statistical evaluation of reproducibility and differential gene expression. Both CAGE and SAGE provided highly reproducible data (Pearson's correlations >0.92 among biological triplicates). With both methods we found around 10,000 genes expressed at levels >2 transcripts per million (approximately 0.3 copies per cell), with an overlap of 86%. We identified 4304 and 3846 genes differentially expressed between proliferating and differentiated C2C12 cells by CAGE and SAGE, respectively, with an overlap of 2144. We identified 196 novel regulatory regions with preferential use in proliferating or differentiated cells. Next-generation sequencing of CAGE and SAGE libraries provides consistent expression levels and can enrich current genome annotations with tissue-specific promoters and alternative 3'-UTR usage.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.