Evidence map›Paper›PMID 41518497›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2026

Identification of Accessible Transcription Factor Binding Sites During the Seed-to-Seedling Transition.

Benjamin J M Tremblay, Julia I Qüesta

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2026. 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

2 authors.

Benjamin J M TremblayCentre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB, Barcelona, Spain.
Julia I QüestaCentre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB, Barcelona, Spain. julia.questa@cragenomica.es.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Germination is a highly dynamic developmental transition from dry quiescent seeds to vegetative seedlings which involves major chromatin rearrangements and changes in transcriptional programs. Assay for transposase-accessible chromatin with sequencing (ATAC-seq) is a quick and reproducible method for quantifying relative chromatin accessibility genome-wide. In this chapter, we describe the use of ATAC-seq for profiling chromatin accessibility changes and differential transcription factor binding site accessibility during germination from enriched embryos.

Indexed as

ArabidopsisGerminationSeedlingsSeedsTranscription FactorsBinding SitesChromatinChromatin Immunoprecipitation SequencingGene Expression Regulation, PlantProtein BindingChromatinTranscription FactorsATAC-seqChromatin accessibilityEmbryosEpigeneticsNucleiSeed germinationTagmentationTranscription factor binding sites

Identifiers

PMID41518497

What Socratic 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 Socratic graph.