Evidence map›Paper›PMID 37540425›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2023

A Workflow Guide to RNA-Seq Analysis of Chaperone Function and Beyond.

Kristina M Holton, Richard M Giadone, Benjamin J Lang, Stuart K Calderwood

Abstract read
PubMed Publisher
In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2023. 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

4 authors.

Kristina M HoltonDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA. kmholton@fas.harvard.edu.
Richard M GiadoneDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
Benjamin J LangDepartment of Radiation Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA.
Stuart K CalderwoodDepartment of Radiation Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

RNA sequencing (RNA-seq) is a powerful method of transcriptional analysis that allows for the sequence identification and quantification of cellular transcripts. RNA-seq can be used for differential gene expression (DGE) analysis, gene fusion detection, allele-specific expression, isoform and splice variant quantification, and identification of novel genes. These applications can be used for downstream systems biology analyses such as gene ontology or pathway analysis to provide insight into processes altered between biological conditions. Given the wide range of signaling pathways subject to chaperone activity as well as numerous chaperone functions in RNA metabolism, RNA-seq may provide a valuable tool for the study of chaperone proteins in biology and disease. This chapter outlines an example RNA-seq workflow to determine differentially expressed (DE) genes between two or more sample conditions and provides some considerations for RNA-seq experimental design.

Indexed as

High-Throughput Nucleotide SequencingMolecular ChaperonesGene Expression ProfilingRNA-SeqSequence Analysis, RNATranscriptomeWorkflowMolecular ChaperonesChaperonesDifferential gene expression analysisGene set enrichment analysisOverrepresentation analysisRNA-seq

Identifiers

PMID37540425

What OpenQuestion holds

Textmetadata
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.