RNA Sequencing Experimental Analysis Workflow Using Caenorhabditis elegans.

Jose Robledo, Saifun Ripa Nahar, Manuel A Ruiz, Raymond J Hendricks, David J Burks, Mary L Ladage, Taegun Kwon, Rajeev K Azad, Pamela A Padilla

Abstract read

PubMed Publisher

In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2024. 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.

PD-1 deficiency reshapes the TCRβ repertoire and T-cell developmental programs associated with susceptibility to lupus-like autoimmunity.Frontiers in immunology · 2026
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

9 authors.

Jose RobledoDepartment of Biological Sciences, University of North Texas, Denton, TX, USA.

Saifun Ripa NaharDepartment of Biological Sciences, University of North Texas, Denton, TX, USA.

Manuel A RuizDepartment of Biological Sciences, University of North Texas, Denton, TX, USA.

Raymond J HendricksDepartment of Biological Sciences, University of North Texas, Denton, TX, USA.

David J BurksDepartment of Biological Sciences, University of North Texas, Denton, TX, USA.

Mary L LadageDepartment of Biological Sciences, University of North Texas, Denton, TX, USA.

Taegun KwonDepartment of Biological Sciences, University of North Texas, Denton, TX, USA.

Rajeev K AzadDepartment of Biological Sciences, University of North Texas, Denton, TX, USA.ORCID 0000-0002-6874-6146

Pamela A PadillaDepartment of Biological Sciences, University of North Texas, Denton, TX, USA. pamela.padilla@unt.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

RNA sequencing is an approach to transcriptomic profiling that enables the detection of differentially expressed genes in response to genetic mutation or experimental treatment, among other uses. Here we describe a method for the use of a customizable, user-friendly bioinformatic pipeline to identify differentially expressed genes in RNA sequencing data obtained from C. elegans, with attention to the improvement in reproducibility and accuracy of results.

Indexed as

Caenorhabditis elegansComputational BiologyGene Expression ProfilingSequence Analysis, RNASoftwareWorkflowAnimalsHigh-Throughput Nucleotide SequencingReproducibility of ResultsTranscriptomeBioinformatic pipelineDifferentially expressed genesReproducibilityRNA sequencing

Identifiers

PMID39068359

DOI10.1007/978-1-4939-7834-2_3

What OpenQuestion holds

Textmetadata

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Registered trials

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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.