ArticlePloS one2012
Automated workflow for preparation of cDNA for cap analysis of gene expression on a single molecule sequencer.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 26 citations in OpenAlex.
- A transformer-based method for the cap analysis of gene expression and gene expression tag associated capping region prediction in RNA.RNA biology · 2026Article
- Third-generation sequencing technology in the prevention and control of thalassemia: Applications and advances.The Journal of international medical research · 2026Review
- Applications of deep learning in understanding gene regulation.Cell reports methods · 2023Review
- Systematic analysis of transcription start sites in avian development.PLoS biology · 2017Article
- FANTOM5 CAGE profiles of human and mouse samples.Scientific data · 2017Article
- Paradigm shifts in genomics through the FANTOM projects.Mammalian genome : official journal of the International Mammalian Genome Society · 2015Article
- Gateways to the FANTOM5 promoter level mammalian expression atlas.Genome biology · 2015Article
- Discovery of molecular markers to discriminate corneal endothelial cells in the human body.PloS one · 2015Article
- Explaining the correlations among properties of mammalian promoters.Nucleic acids research · 2014Article
- Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing.Genome research · 2014Article
- Simultaneous mapping of transcript ends at single-nucleotide resolution and identification of widespread promoter-associated non-coding RNA governed by TATA elements.Nucleic acids research · 2014Article
- Capturing drug responses by quantitative promoter activity profiling.CPT: pharmacometrics & systems pharmacology · 2013Article
Corrections and comments
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Authors and funding
12 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCap analysis of gene expression (CAGE) is a 5' sequence tag technology to globally determine transcriptional starting sites in the genome and their expression levels and has most recently been adapted to the HeliScope single molecule sequencer. Despite significant simplifications in the CAGE protocol, it has until now been a labour intensive protocol. METHODOLOGY: In this study we set out to adapt the protocol to a robotic workflow, which would increase throughput and reduce handling. The automated CAGE cDNA preparation system we present here can prepare 96 'HeliScope ready' CAGE cDNA libraries in 8 days, as opposed to 6 weeks by a manual operator.We compare the results obtained using the same RNA in manual libraries and across multiple automation batches to assess reproducibility.
conclusionsWe show that the sequencing was highly reproducible and comparable to manual libraries with an 8 fold increase in productivity. The automated CAGE cDNA preparation system can prepare 96 CAGE sequencing samples simultaneously. Finally we discuss how the system could be used for CAGE on Illumina/SOLiD platforms, RNA-seq and full-length cDNA generation.
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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.