Evidence map›Paper›PMID 42541720›Full record

ArticleSTAR protocols2026

Protocol for single-cell epigenetic profiling in human organoids and tumoroids with Epi-CyTOF.

Ezgi Senoglu, Vivian Mittné, Sevina Dietz, Anne Eugster, Sebastian Thieme, Franziska Baenke, Mareike Albert, Claudia Peitzsch

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in STAR protocols, 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

8 authors.

Ezgi SenogluCenter for Regenerative Therapies Dresden (CRTD), TUD Dresden University of Technology, 01307 Dresden, Germany. Electronic address: ezgi.senoglu@tu-dresden.de.
Vivian MittnéDepartment of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Dresden University of Technology, 01307 Dresden, Germany. Electronic address: vivian.mittne@ukdd.de.
Sevina DietzCenter for Regenerative Therapies Dresden (CRTD), TUD Dresden University of Technology, 01307 Dresden, Germany.
Anne EugsterCenter for Regenerative Therapies Dresden (CRTD), TUD Dresden University of Technology, 01307 Dresden, Germany.
Sebastian ThiemeDepartment of Pediatrics, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany.
Franziska BaenkeDepartment of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Dresden University of Technology, 01307 Dresden, Germany; National Center for Tumor Diseases (NCT/UCC), 01037 Dresden, a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany; German Cancer Consortium (DKTK), Partner Site Dresden, 01307 Dresden, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
Mareike AlbertCenter for Regenerative Therapies Dresden (CRTD), TUD Dresden University of Technology, 01307 Dresden, Germany.
Claudia PeitzschCenter for Regenerative Therapies Dresden (CRTD), TUD Dresden University of Technology, 01307 Dresden, Germany. Electronic address: claudia.peitzsch@tu-dresden.de.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

In this protocol, we present Epi-CyTOF, a cytometry by time of flight (CyTOF) approach for single-cell epigenome profiling in cortical organoids as a model system for human brain development. We describe steps for in silico panel design, antibody conjugation and testing, sample preparation and staining, and high-dimensional data analysis. Additionally, we provide recommendations for applying Epi-CyTOF to other model systems based on our experience with gastroesophageal tumoroids. For complete details on the use and execution of this protocol, please refer to Ditzer et al .

Indexed as

Bioinformaticscancercell biologydevelopmental biologyGenomicsImmunologymass cytometrymolecular biologyNeuroscienceorganoidssingle cell

Identifiers

PMID42541720
PMCPMC13453457

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LicenceCC BY
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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.