ArticleMethods (San Diego, Calif.)2019
Development of Poly(A)-ClickSeq as a tool enabling simultaneous genome-wide poly(A)-site identification and differential expression analysis.
Article in Methods (San Diego, Calif.), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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
20 citing papers in PubMed.
- Antagonism of stress granules key for SARS-CoV-2 infection and pathogenesis.bioRxiv : the preprint server for biology · 2026Article
- G-quadruplexes in the proximity 3'-UTR enhances alternative polyadenylation of Neogenin 1.iScience · 2025Article
- SARS-CoV-2 EndoU-ribonuclease regulates RNA recombination and impacts viral fitness.Nature communications · 2025Article
- CPSF1 inhibition promotes widespread use of intergenic polyadenylation sites and impairs glycolysis in prostate cancer cells.Cell reports · 2025Article
- Regulation of theRNA (New York, N.Y.) · 2024Article
- Tau mediates the reshaping of the transcriptional landscape toward intermediate Alzheimer's disease stages.Frontiers in cell and developmental biology · 2024Article
- Sex chromosome mechanisms in cardiac development and disease.Nature cardiovascular research · 2023Article
- Alternative polyadenylation alters protein dosage by switching between intronic and 3'UTR sites.Science advances · 2023Article
- Macrophage differentiation is marked by increased abundance of the mRNA 3' end processing machinery, altered poly(A) site usage, and sensitivity to the level of CstF64.Frontiers in immunology · 2023Article
- Zika Virus Infection Alters Gene Expression and Poly-Adenylation Patterns in Placental Cells.Pathogens (Basel, Switzerland) · 2022Article
- QTQTN motif upstream of the furin-cleavage site plays a key role in SARS-CoV-2 infection and pathogenesis.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Generation and characterization of human Fetal membrane and Decidual cell lines for reproductive biology experiments†.Biology of reproduction · 2022Article
- An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability.Nature genetics · 2021Article
- SAM homeostasis is regulated by CFIeLife · 2021Article
- Human Pumilio proteins directly bind the CCR4-NOT deadenylase complex to regulate the transcriptome.RNA (New York, N.Y.) · 2021Article
- A computational pipeline to infer alternative poly-adenylation from 3' sequencing data.Methods in enzymology · 2021Article
- Tau Modulates mRNA Transcription, Alternative Polyadenylation Profiles of hnRNPs, Chromatin Remodeling and Spliceosome Complexes.Frontiers in molecular neuroscience · 2021Article
- PolyA-miner: accurate assessment of differential alternative poly-adenylation from 3'Seq data using vector projections and non-negative matrix factorization.Nucleic acids research · 2020Article
- Partial loss of CFIm25 causes learning deficits and aberrant neuronal alternative polyadenylation.eLife · 2020Article
- DPAC: A Tool for Differential Poly(A)-Cluster Usage from Poly(A)-Targeted RNAseq Data.G3 (Bethesda, Md.) · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
The use of RNA-seq as a generalized tool to measure the differential expression of genes has essentially replaced the use of the microarray. Despite the acknowledged technical advantages to this approach, RNA-seq library preparation remains mostly conducted by core facilities rather than in the laboratory due to the infrastructure, expertise and time required per sample. We have recently described two 'click-chemistry' based library construction methods termed ClickSeq and Poly(A)-ClickSeq (PAC-seq) as alternatives to conventional RNA-seq that are both cost effective and rely on straightforward reagents readily available to most labs. ClickSeq is random-primed and can sequence any (unfragmented) RNA template, while PAC-seq is targeted to poly(A) tails of mRNAs. Here, we further develop PAC-seq as a platform that allows for simultaneous mapping of poly(A) sites and the measurement of differential expression of genes. We provide a detailed protocol, descriptions of appropriate computational pipelines, and a proof-of-principle dataset to illustrate the technique. PAC-seq offers a unique advantage over other 3' end mapping protocols in that it does not require additional purification, selection, or fragmentation steps allowing sample preparation directly from crude total cellular RNA. We have shown that PAC-seq is able to accurately and sensitively count transcripts for differential gene expression analysis, as well as identify alternative poly(A) sites and determine the precise nucleotides of the poly(A) tail boundaries.
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.