Evidence map›Paper›PMID 41051672›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2026

RNA-Seq Analysis in Plant Stress Memory: A Bioinformatics Protocol.

Shivanti Negi, Shagun Sharma, Pankaj Kumar, Mohammad Irfan

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Article in Methods in molecular biology (Clifton, N.J.), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0citing papers in PubMed
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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

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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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

4 authors.

Shivanti NegiDepartment of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India.
Shagun SharmaDepartment of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India.
Pankaj KumarDepartment of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India. pksharmabiotech@yspuniversity.ac.in.
Mohammad IrfanPlant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Understanding plant responses to stress is crucial for improving crop resilience in the face of climate change and environmental challenges. One emerging method for studying these responses is RNA sequencing (RNA-Seq), which comprehensively analyzes transcriptomic changes under various stress conditions. This chapter presents a basic step-by-step bioinformatics protocol for analyzing RNA-Seq data from plants under stress conditions. The protocol covers quality control, read trimming, alignment, gene expression quantification, differential expression analysis, functional enrichment, and interpretation of the results to understand how plants remember and respond to past stress events. The protocol emphasizes the utility of various bioinformatics tools and databases, ensuring reproducibility and clarity in the results. By following these methods, researchers can identify and characterize the genes involved in plant stress memory, paving the way for future advances in plant stress resilience.

Indexed as

Computational BiologyPlantsRNA-SeqSequence Analysis, RNAStress, PhysiologicalGene Expression ProfilingGene Expression Regulation, PlantTranscriptomeBioinformaticsDifferential gene expressionfunctional enrichmentStress resilienceStress responseTranscriptomics

Identifiers

PMID41051672

What OpenQuestion holds

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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.