Evidence map›Paper›PMID 37682474›Full record

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

Estimating DNA-Binding Specificities of Transcription Factors Using SELEX-Seq.

Peilin Chen, Cezary Smaczniak, Johanna Haffner, Jose M Muino, Kerstin Kaufmann

Abstract read
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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
0.8field-weighted citation impact, top 23% of its field
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 citations in OpenAlex.

  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

5 authors at 1 institution in 1 country.

Peilin ChenInstitute for Biology, Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
Cezary SmaczniakInstitute for Biology, Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
Johanna HaffnerInstitute for Biology, Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
Jose M MuinoInstitute for Biology, Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
Kerstin KaufmannInstitute for Biology, Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, Berlin, Germany. kerstin.kaufmann@hu-berlin.de.
Humboldt-Universität zu Berlin · DE

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Here we provide an updated protocol for the Systematic Evolution of Ligands followed by massively parallel sequencing (SELEX-seq) method to study protein-DNA interaction specificities. This in vitro method is used to characterize DNA-binding specificities of transcription factors (TFs). The procedure is based on cycles of immunoprecipitation of protein-DNA complexes, starting with a randomized DNA library of defined fragment length, followed by massively parallel sequencing. The updated protocol includes aspects of experimental design and procedure as well as basic instructions on data analysis.

Indexed as

Data AnalysisTranscription FactorsGene LibraryHigh-Throughput Nucleotide SequencingImmunoprecipitationTranscription FactorsDNA-binding specificityEMSAProtein-DNA interactionsSELEXTranscription factors

Identifiers

PMID37682474
OpenAlexW4386529461

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.