ArticleBMC genomics2015
NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Epigenetic therapy potentiates transposable element transcription to create tumor-enriched antigens in glioblastoma cells.Nature genetics · 2024Article
- Cis-regulatory evolution of the recently expanded Ly49 gene family.Nature communications · 2024Article
- Pan-cancer analysis identifies tumor-specific antigens derived from transposable elements.Nature genetics · 2023Article
- SCAFE: a software suite for analysis of transcribed cis-regulatory elements in single cells.Bioinformatics (Oxford, England) · 2022Article
- Simple and accurate transcriptional start site identification using Smar2C2 and examination of conserved promoter features.The Plant journal : for cell and molecular biology · 2022Article
- Epigenomic analysis reveals prevalent contribution of transposable elements toGenome research · 2022Article
- Bookend: precise transcript reconstruction with end-guided assembly.Genome biology · 2022Article
- Translation initiation landscape profiling reveals hidden open-reading frames required for the pathogenesis of tomato yellow leaf curl Thailand virus.The Plant cell · 2022Article
- Chemical capping improves template switching and enhances sequencing of small RNAs.Nucleic acids research · 2022Article
- Genome-Wide Profiling of Transcription Initiation with STRIPE-seq.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Global approaches for profiling transcription initiation.Cell reports methods · 2021Review
- Flexible analysis of TSS mapping data and detection of TSS shifts with TSRexploreR.NAR genomics and bioinformatics · 2021Article
- Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq.Genome research · 2020Article
- Non-templated addition and template switching by Moloney murine leukemia virus (MMLV)-based reverse transcriptases co-occur and compete with each other.The Journal of biological chemistry · 2019Article
- CAGEfightR: analysis of 5'-end data using R/Bioconductor.BMC bioinformatics · 2019Article
- An Overview of Methodologies in Studying lncRNAs in the High-Throughput Era: When Acronyms ATTACK!Methods in molecular biology (Clifton, N.J.) · 2019Article
- NanoPARE: parallel analysis of RNA 5' ends from low-input RNA.Genome research · 2018Article
- Comprehensive comparative analysis of 5'-end RNA-sequencing methods.Nature methods · 2018Article
- A systemic identification approach for primary transcription start site of Arabidopsis miRNAs from multidimensional omics data.Functional & integrative genomics · 2017Article
- Small Genetic Circuits and MicroRNAs: Big Players in Polymerase II Transcriptional Control in Plants.The Plant cell · 2016Review
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Authors and funding
3 authors.
Funding
Abstract
backgroundIdentifying the transcription start sites (TSS) of genes is essential for characterizing promoter regions. Several protocols have been developed to capture the 5' end of transcripts via Cap Analysis of Gene Expression (CAGE) or linker-ligation strategies such as Paired-End Analysis of Transcription Start Sites (PEAT), but often require large amounts of tissue. More recently, nanoCAGE was developed for sequencing on the Illumina GAIIx to overcome these difficulties.
resultsHere we present the first publicly available adaptation of nanoCAGE for sequencing on recent ultra-high throughput platforms such as Illumina HiSeq-2000, and CapFilter, a computational pipeline that greatly increases confidence in TSS identification. We report excellent gene coverage, reproducibility, and precision in transcription start site discovery for samples from Arabidopsis thaliana roots.
conclusionnanoCAGE-XL together with CapFilter allows for genome wide identification of high confidence transcription start sites in large eukaryotic genomes.
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