Evidence map›Paper›PMID 37191807›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2023

Single-Cell and Spatial Analysis of Emergent Organoid Platforms.

Aditi Kumar, Shuangyi Cai, Mayar Allam, Samuel Henderson, Melissa Ozbeyler, Lilly Saiontz, Ahmet F Coskun

Abstract read
PubMed Publisher
In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 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
–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

1 citing paper in PubMed.

  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.

Aditi KumarWallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
Shuangyi CaiWallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
Mayar AllamWallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
Samuel HendersonWallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
Melissa OzbeylerWallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
Lilly SaiontzWallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
Ahmet F CoskunWallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA. ahmet.coskun@bme.gatech.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Organoids have emerged as a promising advancement of the two-dimensional (2D) culture systems to improve studies in organogenesis, drug discovery, precision medicine, and regenerative medicine applications. Organoids can self-organize as three-dimensional (3D) tissues derived from stem cells and patient tissues to resemble organs. This chapter presents growth strategies, molecular screening methods, and emerging issues of the organoid platforms. Single-cell and spatial analysis resolve organoid heterogeneity to obtain information about the structural and molecular cellular states. Culture media diversity and varying lab-to-lab practices have resulted in organoid-to-organoid variability in morphology and cell compositions. An essential resource is an organoid atlas that can catalog protocols and standardize data analysis for different organoid types. Molecular profiling of individual cells in organoids and data organization of the organoid landscape will impact biomedical applications from basic science to translational use.

Indexed as

OrganoidsRegenerative MedicineHumansOrganogenesisSpatial AnalysisStem CellsAdult stem cells (ASCs)Cyclic immunofluorescence (CycIF)Embryonic stem cells (ESCs)Epi-illumination selective-plane illumination microscope (eSPIM)Extracellular matrix (ECM)High-dimensional immunophenotypingImaging mass cytometry (IMC)Induced pluripotent stem cells (iPSC)Light-sheet fluorescence microscopy (LSFM)Matrix-assisted laser desorption/ionization (MALDI)Multiplexed error-robust fluorescence in situ hybridization (MERFISH)Multivariate-barcoded mass cytometry (MC)Open-top light-sheet (OTLS) microscopesOrganogenesisOrganoid atlasOrganoid heterogeneityPatient-derived xenograft (PDX)Pluripotent stem cells (PSCs)Precision medicineRegenerative medicineSequential fluorescence in situ hybridization (seqFISH)Single-cell and spatial analysisSingle-cell RNA-sequencing (scRNA-seq)Three-dimensional (3D) tissuesTime-of-flight secondary ion mass spectrometry (TOF-SIMS)

Identifiers

PMID37191807

What OpenQuestion holds

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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.