Evidence map›Paper›PMID 37393374›Full record

ArticleScientific reports2023

Single cell RNA analysis of the left-right organizer transcriptome reveals potential novel heterotaxy genes.

Helen M Bellchambers, Amruta R Phatak, Mardi J Nenni, Maria B Padua, Hongyu Gao, Yunlong Liu, Stephanie M Ware

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

Article in Scientific reports, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
0.6field-weighted citation impact, top 30% 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

3 citing papers in PubMed, 4 citations in OpenAlex.

  1. Article
  2. Review
  3. 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 2 institutions in 1 country.

Helen M Bellchambers *Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, 1044 W. Walnut Street, Indianapolis, IN, 46202, USA.ORCID 0000-0002-3164-4197
Amruta R Phatak *Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, 1044 W. Walnut Street, Indianapolis, IN, 46202, USA.
Mardi J NenniDivision of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.ORCID 0000-0002-6238-1932
Maria B PaduaHerman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, 1044 W. Walnut Street, Indianapolis, IN, 46202, USA.ORCID 0000-0002-9539-422X
Hongyu GaoDepartment of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
Yunlong LiuDepartment of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.ORCID 0000-0002-2699-626X
Stephanie M WareHerman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, 1044 W. Walnut Street, Indianapolis, IN, 46202, USA. stware@iu.edu.ORCID 0000-0003-4714-0142
Indiana University School of MedicineCincinnati Children's Hospital Medical Center · US

Funding

Quality Assurance and Quality Control Project Management: Improving Submissions and Study Conduct in the Human Subjects Research Prior Approval ProcessUL1TR002529 · NCATS · INDIANA UNIVERSITY INDIANAPOLIS · PI MOE, SHARON M, WIEHE, SARAH ELIZABETH · 2018 to 2022
$27.2M
Transcriptional regulation of cardiac morphogenesisP01HL134599 · NHLBI · INDIANA UNIVERSITY INDIANAPOLIS · PI Anthony B. Firulli · 2017 to 2026
$25.7M
Role of the Embryonic Node in Cardiac Development and Congenital Heart DiseaseR01HL088639 · NHLBI · CINCINNATI CHILDRENS HOSP MED CTR · PI WARE, STEPHANIE M · 2007 to 2011
$2.0M
NCATS NIH HHS UL1 TR002529NHLBI NIH HHS P01 HL134599NHLBI NIH HHS R01 HL088639
6 · The paper itself

Abstract

The establishment of left-right patterning in mice occurs at a transient structure called the embryonic node or left-right organizer (LRO). Previous analysis of the LRO has proven challenging due to the small cell number and transient nature of this structure. Here, we seek to overcome these difficulties to define the transcriptome of the LRO. Specifically, we used single cell RNA sequencing of 0-1 somite embryos to identify LRO enriched genes which were compared to bulk RNA sequencing of LRO cells isolated by fluorescent activated cell sorting. Gene ontology analysis indicated an enrichment of genes associated with cilia and laterality terms. Furthermore, comparison to previously identified LRO genes identified 127 novel LRO genes, including Ttll3, Syne1 and Sparcl1, for which the expression patterns were validated using whole mount in situ hybridization. This list of novel LRO genes will be a useful resource for further studies on LRO morphogenesis, the establishment of laterality and the genetic causes of heterotaxy.

Indexed as

CiliaTranscriptomeAnimalsCalcium-Binding ProteinsCell CountCell SeparationExtracellular Matrix ProteinsMiceRNACalcium-Binding ProteinsExtracellular Matrix ProteinsRNASparcl1 protein, mouse

Identifiers

PMID37393374
PMCPMC10314903
OpenAlexW4382810543

What OpenQuestion holds

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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.