Evidence map›Paper›PMID 37477440›Full record

ArticlemSystems2023

Transcriptome architecture of the three main lineages of agrobacteria.

Lucas Waldburger, Mitchell G Thompson, Alexandra J Weisberg, Namil Lee, Jeff H Chang, Jay D Keasling, Patrick M Shih

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in mSystems, 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
0.4field-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

7 authors at 3 institutions in 3 countries.

Lucas WaldburgerDepartment of Bioengineering, University of California , Berkeley, California, USA.ORCID 0000-0002-4735-5285
Mitchell G ThompsonJoint BioEnergy Institute , Emeryville, California, USA.
Alexandra J WeisbergDepartment of Botany and Plant Pathology, Oregon State University , Corvallis, Oregon, USA.ORCID 0000-0002-0045-1368
Namil LeeJoint BioEnergy Institute , Emeryville, California, USA.
Jeff H ChangDepartment of Botany and Plant Pathology, Oregon State University , Corvallis, Oregon, USA.
Jay D KeaslingJoint BioEnergy Institute , Emeryville, California, USA.ORCID 0000-0003-4170-6088
Patrick M ShihJoint BioEnergy Institute , Emeryville, California, USA.ORCID 0000-0002-2119-3345
Lawrence Berkeley National Laboratory · USOregon State University · USQB3 · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Agrobacteria are a diverse, polyphyletic group of prokaryotes with multipartite genomes capable of transferring DNA into the genomes of host plants, making them an essential tool in plant biotechnology. Despite their utility in plant transformation, genome-wide transcriptional regulation is not well understood across the three main lineages of agrobacteria. Transcription start sites (TSSs) are a necessary component of gene expression and regulation. In this study, we used differential RNA-seq and a TSS identification algorithm optimized on manually annotated TSS, then validated with existing TSS to identify thousands of TSS with nucleotide resolution for representatives of each lineage. We extend upon the 356 TSSs previously reported in

Indexed as

GenomicsTranscriptomeGene Expression RegulationNucleotidesPromoter Regions, GeneticNucleotidesagrobacteriumcomparative transcriptomicsdifferential RNA-seqevolutionpathogenesistranscription start sites

Identifiers

PMID37477440
PMCPMC10469942
OpenAlexW4384922558

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.