Evidence map›Paper›PMID 39141238›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2024

Integrative Analysis of CUT&Tag and RNA-Seq Data Through Bioinformatics: A Unified Workflow for Enhanced Insights.

Niccolò Liorni, Alessandro Napoli, Marta Adinolfi, Manlio Vinciguerra, Tommaso Mazza

Abstract read
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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. Not yet cited in PubMed.

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

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

5 authors.

Niccolò LiorniBioinformatics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy.
Alessandro NapoliBioinformatics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy.
Marta AdinolfiBioinformatics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy.
Manlio VinciguerraDepartment of Translational Stem Cell Biology, Research Institute of the Medical University, Varna, Bulgaria. manlio.vinciguerra@mu-varna.bg.
Tommaso MazzaBioinformatics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Cleavage Under Targets and Tagmentation (CUT&Tag) is a recent methodology used for robust epigenomic profiling that, unlike conventional chromatin immunoprecipitation (ChIP-Seq), requires only a limited amount of cells as starting material. RNA sequencing (RNA-Seq) reveals the presence and quantity of RNA in a biological sample, describing the continuously changing cellular transcriptome. The integrated analysis of transcriptional activity, histone modifications, and chromatin accessibility via CUT&Tag is still in its infancy compared to the well-established ChIP-Seq. This chapter describes a robust bioinformatics methodology and workflow to perform an integrative CUT&Tag/RNA-Seq analysis.

Indexed as

Computational BiologyWorkflowChromatinChromatin ImmunoprecipitationChromatin Immunoprecipitation SequencingEpigenomicsGene Expression ProfilingHigh-Throughput Nucleotide SequencingHumansRNA-SeqSequence Analysis, RNASoftwareTranscriptomeChromatinBioinformaticsChromatin immunoprecipitation sequencing (ChIP-Seq)Cleavage under targets and tagmentation (CUT&Tag)Histone marksNext-generation sequencing (NGS)RNA sequencing (RNA-Seq)

Identifiers

PMID39141238

What OpenQuestion holds

Textmetadata
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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.