Evidence map›Paper›PMID 40960013›Full record

ArticleDevelopment (Cambridge, England)2025

Automated, high-throughput in situ hybridization of sea urchin (Lytechinus pictus) embryos.

Yoon Lee, Chloe Jenniches, Rachel Metry, Gloria Renaudin, Svenja Kling, Evan Tjeerdema, Elliot W Jackson, Amro Hamdoun

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Development (Cambridge, England), 2025. 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
–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

3 citing papers in PubMed.

  1. Cryopreservation of sea urchin (Lytechinus pictus) embryos and development through metamorphosis.Developmental dynamics : an official publication of the American Association of Anatomists · 2026
    Article
  2. The tuxedo sea urchinbioRxiv : the preprint server for biology · 2026
    Article
  3. Efficient Endogenous Tagging in the Sea Urchin,bioRxiv : the preprint server for biology · 2026
    Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

8 authors.

Yoon LeeCenter for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA.ORCID 0000-0003-0147-3208
Chloe JennichesCenter for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA.ORCID 0009-0000-9955-393X
Rachel MetryCenter for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA.ORCID 0000-0002-6156-5799
Gloria RenaudinCenter for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA.ORCID 0009-0009-7909-7733
Svenja KlingCenter for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA.ORCID 0000-0001-5109-2521
Evan TjeerdemaCenter for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA.ORCID 0000-0003-3732-9232
Elliot W JacksonCenter for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA.ORCID 0000-0002-4213-3851
Amro HamdounCenter for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA.ORCID 0000-0003-2568-048X

Funding

Scripps Center for Oceans and Human Health: advancing the science of marine contaminants and seafood securityP01ES035541 · NIEHS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI AMRO M HAMDOUN, BRADLEY S MOORE · 2024 to 2026
$2.4M
Allen Foundation Allen Discovery CenterIlluminaNational Science FoundationNational Science Foundation 2414798NIEHS NIH HHS ES035541NIEHS NIH HHS P01 ES035541NIH HHSPaul G. Allen Frontiers GroupUniversity of California
6 · The paper itself

Abstract

Despite the reach of in situ hybridization (ISH) in developmental biology, it is rarely used at scale. The major bottleneck is the throughput of the assay, which relies upon labor-intensive manual steps. The goal of this study was to develop a high-throughput, automated hybridization chain reaction (HCR) pipeline for the sea urchin (Lytechinus pictus). Our method, which we term high-throughput (HT)-HCR, can process 192 gene probe sets on whole-mount embryos within 32 h. The physical properties of sea urchin embryos enabled us to utilize a 96-well plate format, miniaturized reaction volumes, a general-purpose robotic liquid handler and automated confocal microscopy. Using this approach, we produced high quality localization data for 101 target genes across three developmental stages. The results reveal the localization of previously undescribed physiological genes, as well as canonical developmental transcription factors. HT-HCR represents an order of magnitude increase in the throughput of spatial expression profiling studies utilizing the sea urchin. This will enable more-sophisticated perturbation analyses and drug-screening efforts in this emerging animal model.

Indexed as

Embryo, NonmammalianHigh-Throughput Screening AssaysIn Situ HybridizationLytechinusSea UrchinsAnimalsGene Expression ProfilingGene Expression Regulation, DevelopmentalHigh-throughputHybridization chain reaction (HCR)In situ hybridization (ISH)Lytechinus pictusSea urchinSpatial transcriptomicsTranscription factorTransporter

Identifiers

PMID40960013
PMCPMC12516323

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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.