Evidence map›Paper›PMID 39028503›Full record

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

Genomic SELEX Screening of Regulatory Targets of Transcription Factors.

Tomohiro Shimada, Hiroshi Ogasawara, Ikki Kobayashi, Akira Ishihama

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 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. 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.

Tomohiro ShimadaMeiji University, School of Agriculture, Kawasaki, Kanagawa, Japan. tomoshimada@meiji.ac.jp.
Hiroshi OgasawaraResearch Center for Advanced Science and technology, Division of Gene Research, Shinshu University, Ueda, Nagano, Japan.
Ikki KobayashiMeiji University, School of Agriculture, Kawasaki, Kanagawa, Japan.
Akira IshihamaResearch Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The genome of Escherichia coli K-12 is transcribed by a single species of RNA polymerase. The selectivity of transcriptional targets is determined via interaction with one of seven species of the sigma subunit and a total of approximately 300 species of transcription factor (TFs). For comprehensive identification of the regulatory targets of these two groups of regulatory proteins on the genome, we developed an in vitro approach, "Genomic SELEX" (gSELEX) screening. Here we describe a detailed protocol of the gSELEX screening system, which uses purified regulatory proteins and fragments of genomic DNA from E. coli. Moreover, we describe methods and examples of results using cell-free synthetic proteins.

Indexed as

SELEX Aptamer TechniqueTranscription FactorsEscherichia coliEscherichia coli K12Escherichia coli ProteinsGenome, BacterialGenomicsEscherichia coli ProteinsTranscription FactorsDNA-protein interactionEscherichia coliGenomic SELEXRegulatory targetRNA polymeraseSigma factorTranscription factor

Identifiers

PMID39028503

What OpenQuestion holds

Textmetadata
Read underepoch 390

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.