ArticleNature methods2018
Comprehensive comparative analysis of 5'-end RNA-sequencing methods.
Article in Nature methods, 2018. 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 80 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
80 citing papers in PubMed.
- A transformer-based method for the cap analysis of gene expression and gene expression tag associated capping region prediction in RNA.RNA biology · 2026Article
- Article
- Review
- Intrinsic promoter responsiveness dictates sensitivity to transcriptional activation by enhancers.bioRxiv : the preprint server for biology · 2026Article
- Heavy-chain immune repertoire sequencing enables language-model prediction of antigen-specific antibodies.Research square · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Profiling active RNA polymerase II transcription start sites from total RNA by capped small RNA sequencing (csRNA-seq).Nature protocols · 2026Review
- Transcript diversity reflects deleterious RNA processing errors shaped by population size in metazoans.PLoS biology · 2026Article
- Exploring single-cell and multi-omics technologies and their role in unraveling tumor heterogeneity of hepatocellular carcinoma.Journal of liver cancer · 2026Review
- Elucidating the coordination of RNA processing using short-read and long-read RNA-sequencing methods.Nature reviews. Molecular cell biology · 2026Review
- CRAGE-RB-PI-seq reveals transcriptional dynamics of plant-associated bacteria during root colonization.Nature communications · 2026Article
- The Inevitable Relationship Between Viruses and RNA Modifications Revealed Through Adenovirus Research.Viruses · 2026Review
- A practical guide to targeted single-cell RNA sequencing technologies.Communications biology · 2026Review
- Advancements in single-cell sequencing for cervical cancer research.Molecular and cellular biochemistry · 2026Review
- Comparative TSS-seq analysis among natural variations ofNAR genomics and bioinformatics · 2025Article
- Alternative transcription increases isoform complexity in Long Non-Coding RNAs and alters their functions in cancer.Non-coding RNA research · 2025Review
- Chromosome-Contiguous Reference Genome forInternational journal of molecular sciences · 2025Article
- Disruption of TAD hierarchy promotes LTR co-option in cancer.Nature genetics · 2025Article
- RNA multi-omics in single cells reveal rhythmical RNA reshaping during human and mouse oocyte maturation.BMC biology · 2025Article
- Decoding meLife · 2025Article
20 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
12 authors.
Funding
Abstract
Specialized RNA-seq methods are required to identify the 5' ends of transcripts, which are critical for studies of gene regulation, but these methods have not been systematically benchmarked. We directly compared six such methods, including the performance of five methods on a single human cellular RNA sample and a new spike-in RNA assay that helps circumvent challenges resulting from uncertainties in annotation and RNA processing. We found that the 'cap analysis of gene expression' (CAGE) method performed best for mRNA and that most of its unannotated peaks were supported by evidence from other genomic methods. We applied CAGE to eight brain-related samples and determined sample-specific transcription start site (TSS) usage, as well as a transcriptome-wide shift in TSS usage between fetal and adult brain.
Indexed as
Identifiers
What OpenQuestion holds
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.