Evidence map›Paper›PMID 39284854›Full record

ArticleScientific reports2024

Improving rigor and reproducibility in western blot experiments with the blotRig analysis.

Cleopa Omondi, Austin Chou, Kenneth A Fond, Kazuhito Morioka, Nadine R Joseph, Jeffrey A Sacramento, Emma Iorio, Abel Torres-Espin, Hannah L Radabaugh, Jacob A Davis and 3 more

Abstract read
In one paragraph

Article in Scientific reports, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing 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

8 citing papers in PubMed.

  1. Review
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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

13 authors.

Cleopa OmondiWeill Institute for Neurosciences, University of California, San Francisco, CA, USA.
Austin ChouWeill Institute for Neurosciences, University of California, San Francisco, CA, USA.
Kenneth A FondWeill Institute for Neurosciences, University of California, San Francisco, CA, USA.
Kazuhito MoriokaWeill Institute for Neurosciences, University of California, San Francisco, CA, USA.
Nadine R JosephWeill Institute for Neurosciences, University of California, San Francisco, CA, USA.
Jeffrey A SacramentoWeill Institute for Neurosciences, University of California, San Francisco, CA, USA.
Emma IorioWeill Institute for Neurosciences, University of California, San Francisco, CA, USA.
Abel Torres-EspinWeill Institute for Neurosciences, University of California, San Francisco, CA, USA.
Hannah L RadabaughWeill Institute for Neurosciences, University of California, San Francisco, CA, USA.
Jacob A DavisWeill Institute for Neurosciences, University of California, San Francisco, CA, USA.
Jason H GumbelWeill Institute for Neurosciences, University of California, San Francisco, CA, USA.
J Russell HuieWeill Institute for Neurosciences, University of California, San Francisco, CA, USA. Russell.huie@ucsf.edu.
Adam R FergusonWeill Institute for Neurosciences, University of California, San Francisco, CA, USA. adam.ferguson@ucsf.edu.

Funding

Tools for Common Data Element Adoption in the Pan-Neurotrauma Data Commons (PANORAUMA)U24NS122732 · NINDS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ADAM R FERGUSON, Jeffrey S. Grethe · 2021 to 2026
$5.0M
Maladaptive Plasticity in Spinal Cord Injury: Cellular MechanismsR01NS122888 · NINDS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI FERGUSON, ADAM R · 2021 to 2025
$3.0M
Maladaptive Plasticity in Spinal Cord Injury: Cellular MechanismsR01NS088475 · NINDS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI FERGUSON, ADAM R · 2015 to 2019
$1.7M
SCI Consortium Study: Harnessing big-data for plasticity and rehabilitation in translational SCII01RX002245 · VA · VETERANS AFFAIRS MED CTR SAN FRANCISCO · PI ADAM R FERGUSON · 2017 to 2026
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PRECISE-TBI: PRE Clinical lnteragency research resourcE-TBII50BX005878 · VA · VETERANS HEALTH ADMINISTRATION · PI C EDWARD DIXON, ADAM R FERGUSON · 2022 to 2026
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BLRD VA I01 BX005871BLRD VA I50 BX005878National Institutes of Health/National Institute of Neurological Disorders and Stroke grant R01NS088475NIH NINDS R01NS122888NINDS NIH HHS R01 NS088475NINDS NIH HHS R01 NS122888NINDS NIH HHS U24 NS122732RRD VA I01 RX002245RRD VA I01 RX002787US Veterans Affairs (VA I50BX005878US Veterans Affairs (VA) I01RX002245
6 · The paper itself

Abstract

Western blot is a popular biomolecular analysis method for measuring the relative quantities of independent proteins in complex biological samples. However, variability in quantitative western blot data analysis poses a challenge in designing reproducible experiments. The lack of rigorous quantitative approaches in current western blot statistical methodology may result in irreproducible inferences. Here we describe best practices for the design and analysis of western blot experiments, with examples and demonstrations of how different analytical approaches can lead to widely varying outcomes. To facilitate best practices, we have developed the blotRig tool for designing and analyzing western blot experiments to improve their rigor and reproducibility. The blotRig application includes functions for counterbalancing experimental design by lane position, batch management across gels, and analytics with covariates and random effects.

Indexed as

Blotting, WesternHumansReproducibility of ResultsResearch DesignSoftwareAnalytical chemistryAntibodiesBiostatisticsComputational biologyComputational chemistryWestern blot

Identifiers

PMID39284854
PMCPMC11405887

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

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.