Evidence map›Paper›PMID 34183124›Full record

ArticleMethods in enzymology2021

Quantifying alternative polyadenylation in RNAseq data with LABRAT.

Austin E Gillen, Raeann Goering, J Matthew Taliaferro

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Methods in enzymology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

3 authors.

Austin E GillenDivision of Hematology, University of Colorado School of Medicine, Aurora, CO, United States.
Raeann GoeringDepartment of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States; RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.
J Matthew TaliaferroDepartment of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States; RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, United States. Electronic address: matthew.taliaferro@cuanschutz.edu.

Funding

Metabolomics Technologies to Advance Biomedical ResearchR35GM130385 · NIGMS · SCRIPPS RESEARCH INSTITUTE, THE · PI GARY E SIUZDAK · 2019 to 2026
$3.9M
Predoctoral Training Program in Molecular and Cellular Biology (Supplement: Mentoring in the Research Environment)T32GM136444 · NIGMS · UNIVERSITY OF COLORADO DENVER · PI MICHAEL A MCMURRAY, Rytis Prekeris · 2020 to 2026
$3.7M
Understanding the regulatory language of RNA localizationR35GM133385 · NIGMS · UNIVERSITY OF COLORADO DENVER · PI Jefferson Matthew Taliaferro · 2019 to 2026
$3.4M
Predoctoral Training Program in Molecular BiologyT32GM008730 · NIGMS · UNIVERSITY OF COLORADO DENVER · PI PREKERIS, RYTIS, SCLAFANI, ROBERT A · 1999 to 2019
$3.3M
Deciphering the nanomaterial uptake in a bystander manner invoked by co-administration of functionalized nanoparticlesR01GM133885 · NIGMS · UNIVERSITY OF MINNESOTA · PI PANG, HONGBO · 2019 to 2022
$1.2M
NIGMS NIH HHS R01 GM133885NIGMS NIH HHS R35 GM130385NIGMS NIH HHS R35 GM133385NIGMS NIH HHS T32 GM008730NIGMS NIH HHS T32 GM136444
6 · The paper itself

Abstract

Alternative polyadenylation (APA) generates transcript isoforms that differ in their 3' UTR content and may therefore be subject to different regulatory fates. Although the existence of APA has been known for decades, quantification of APA isoforms from high-throughput RNA sequencing data has been difficult. To facilitate the study of APA in large datasets, we developed an APA quantification technique called LABRAT (Lightweight Alignment-Based Reckoning of Alternative Three-prime ends). LABRAT leverages modern transcriptome quantification approaches to determine the relative abundances of APA isoforms. In this manuscript we describe how LABRAT produces its calculations, provide a step-by-step protocol for its use, and demonstrate its ability to quantify APA in single-cell RNAseq data.

Indexed as

PolyadenylationTranscriptome3' Untranslated RegionsHigh-Throughput Nucleotide SequencingProtein Isoforms3' Untranslated RegionsProtein Isoforms3′ UTR regulationAlternative polyadenylationPost-transcriptional regulationSingle cell RNAseqTranscriptomics

Identifiers

PMID34183124
PMCPMC9041098

What OpenQuestion holds

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Registered trials

None linked

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.