ArticleCold Spring Harbor protocols2011
NanoCAGE: a high-resolution technique to discover and interrogate cell transcriptomes.
Article in Cold Spring Harbor protocols, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 45 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
45 citing papers in PubMed.
- Epigenetic therapy potentiates transposable element transcription to create tumor-enriched antigens in glioblastoma cells.Nature genetics · 2024Article
- Pan-cancer analysis identifies tumor-specific antigens derived from transposable elements.Nature genetics · 2023Article
- Promoter-pervasive transcription causes RNA polymerase II pausing to boost DOG1 expression in response to salt.The EMBO journal · 2023Article
- Simple and accurate transcriptional start site identification using Smar2C2 and examination of conserved promoter features.The Plant journal : for cell and molecular biology · 2022Article
- Cap analysis of gene expression (CAGE) and noncoding regulatory elements.Seminars in immunopathology · 2022Review
- TSSr: an R package for comprehensive analyses of TSS sequencing data.NAR genomics and bioinformatics · 2021Article
- To cap it all off, again: dynamic capping and recapping of coding and non-coding RNAs to control transcript fate and biological activity.Cell cycle (Georgetown, Tex.) · 2021Review
- Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage.Genome research · 2021Article
- Computational annotation of miRNA transcription start sites.Briefings in bioinformatics · 2021Review
- De novo activated transcription of inserted foreign coding sequences is inheritable in the plant genome.PloS one · 2021Article
- The eukaryotic translation initiation factor eIF4E elevates steady-state mProceedings of the National Academy of Sciences of the United States of America · 2020Article
- Methodologies for Transcript Profiling Using Long-Read Technologies.Frontiers in genetics · 2020Review
- FFPEcap-seq: a method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples.Genome research · 2019Article
- Transposable elements drive widespread expression of oncogenes in human cancers.Nature genetics · 2019Article
- Depletion of Hemoglobin Transcripts and Long-Read Sequencing Improves the Transcriptome Annotation of the Polar Bear (Frontiers in genetics · 2019Article
- Analysis of public RNA-sequencing data reveals biological consequences of genetic heterogeneity in cell line populations.Scientific reports · 2018Article
- Comprehensive comparative analysis of 5'-end RNA-sequencing methods.Nature methods · 2018Article
- Tn5Prime, a Tn5 based 5' capture method for single cell RNA-seq.Nucleic acids research · 2018Article
- Reactivation of endogenous retroviral elements via treatment with DNMT- and HDAC-inhibitors.Cell cycle (Georgetown, Tex.) · 2018Review
- mTOR-sensitive translation: Cleared fog reveals more trees.RNA biology · 2017Review
Corrections and comments
- Erratum issuedMizuho, Sakai [corrected to Sakai, Mizuho]
Authors and funding
5 authors.
Funding
Abstract
Cap analysis gene expression (CAGE) is a method to identify the 5' ends of transcripts, allowing the discovery of new promoters and the quantification of gene activity. Combining promoter location and their expression levels, CAGE data are essential for annotation-agnostic studies of regulatory gene networks. However, CAGE requires large amounts of input RNA, which usually are not obtainable from highly refined samples such as tissue microdissections or subcellular fractions. The nanoCAGE method can capture the 5' ends of transcripts from as little as 10 ng of total RNA and takes advantage of the capacity of current sequencers to produce longer (50-100 bp) reads. The method prepares cap-selected cDNAs ready for direct sequencing of their 5' ends (optionally mate-paired with the 3' end) that can provide information about downstream sequences. This protocol describes how to prepare nanoCAGE libraries from as little as 50 ng of total RNA within two working days. The libraries can be sequenced using an Illumina sequencer Genome Analyzer IIX [corrected] with a level of sensitivity 1000 times higher than CAGE.
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Registered trials
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.