Evidence map›Paper›PMID 40934073›Full record

ArticleSTAR protocols2025

Protocol for multiplexed transcription factor activity detection using optimized barcoded reporters and an automated computational pipeline.

Max Trauernicht, Vinícius H Franceschini-Santos, Hatice Yücel, Bas van Steensel

Erratum issuedAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in STAR protocols, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. 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

5 · Who and what money

Authors and funding

4 authors.

Max TrauernichtOncode Institute, Division of Molecular Genetics, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.
Vinícius H Franceschini-SantosOncode Institute, Division of Molecular Genetics, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.
Hatice YücelOncode Institute, Division of Molecular Genetics, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands. Electronic address: h.yucel@nki.nl.
Bas van SteenselOncode Institute, Division of Molecular Genetics, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands. Electronic address: b.v.steensel@nki.nl.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Transcription factors (TFs) regulate the genome in response to signaling events. Detecting their activity is crucial to deciphering the regulatory networks of cells. Here, we present a protocol for multiplexed TF activity detection using a barcoded plasmid library of optimized "prime" TF reporters in cultured cells. We describe steps for library transfection, RNA processing for barcode sequencing, and a computational pipeline for analyzing differential TF activity, enabling high-throughput and quantitative TF profiling. For complete details on the use and execution of this protocol, please refer to Trauernicht et al.

Indexed as

Computational BiologyTranscription FactorsGene LibraryHigh-Throughput Nucleotide SequencingHumansTransfectionTranscription FactorsBioinformaticsCell BiologyCell cultureGene ExpressionGenomicsMolecular BiologyRNAseqSequence analysisSequencingSystems biology

Identifiers

PMID40934073
PMCPMC12491162

What Socratic holds

Textmetadata
LicenceCC BY-NC-ND
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 Socratic graph.