Evidence map›Paper›PMID 40040474›Full record

ArticleZebrafish2025

An Improved, High-Yield Method for Isolating Nuclei from Individual Zebrafish Embryos for Single-Nucleus RNA Sequencing.

Clifford Rostomily, Heidi Lee, Amy Tresenrider, Riza Daza, Andrew Mullen, Jay Shendure, David Kimelman, Cole Trapnell

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Zebrafish, 2025. 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

8 authors.

Clifford RostomilyDepartment of Genome Sciences, University of Washington, Seattle, Washington, USA.
Heidi LeeDepartment of Genome Sciences, University of Washington, Seattle, Washington, USA.
Amy TresenriderDepartment of Genome Sciences, University of Washington, Seattle, Washington, USA.
Riza DazaDepartment of Genome Sciences, University of Washington, Seattle, Washington, USA.
Andrew MullenDepartment of Genome Sciences, University of Washington, Seattle, Washington, USA.
Jay ShendureDepartment of Genome Sciences, University of Washington, Seattle, Washington, USA.
David KimelmanDepartment of Genome Sciences, University of Washington, Seattle, Washington, USA.
Cole TrapnellDepartment of Genome Sciences, University of Washington, Seattle, Washington, USA.

Funding

Versatile, exponentially scalable methods for single cell molecular profilingR01HG010632 · NHGRI · UNIVERSITY OF WASHINGTON · PI Jay Ashok Shendure, Bruce Colston Trapnell · 2019 to 2026
$5.9M
New software tools for differential analysis of single-cell genomics perturbation experimentsR01HG012761 · NHGRI · UNIVERSITY OF WASHINGTON · PI David Kimelman, Bruce Colston Trapnell · 2023 to 2026
$2.5M
NHGRI NIH HHS R01 HG010632NHGRI NIH HHS R01 HG012761
6 · The paper itself

Abstract

Zebrafish is an ideal system to study the effect(s) of chemical, genetic, and environmental perturbations on development due to their high fecundity and fast growth. Recently, single-cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole-embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here, we report a method for efficiently isolating high-quality nuclei from zebrafish embryos in a 96-well plate format by bead homogenization in a lysis buffer. Through head-to-head single-cell combinatorial indexing RNAseq experiments, we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.

Indexed as

Cell NucleusSequence Analysis, RNASingle-Cell AnalysisZebrafishAnimalsEmbryo, NonmammalianembryoisolationnucleiRNAscRNAseqsingle-cellsingle-nuclei

Identifiers

PMID40040474
PMCPMC12167839

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.