OrganoidDB: a comprehensive organoid database for the multi-perspective exploration of bulk and single-cell transcriptomic profiles of organoids
Explore this paper's citation graph
Summary
The introduction of OrganoidDB will facilitate a better understanding of organoids and help improve organoid culture protocols to yield organoids that are highly similar to living organs in terms of composition, architecture and function.
- Type
- article
- Published
- 2022-10-22
- Cited by
- 22
- References
- 40
- Access
- Open access
- OpenAlex
- https://openalex.org/W4307092668
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:253063861
Keywords
Organoid, Biology, Transcriptome, Induced pluripotent stem cell, Computational biology
References
- CellMarker: a manually curated resource of cell markers in human and mouse
- The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans
- The DeLone and McLean Model of Information Systems Success: A Ten-Year Update
- Development of an instrument measuring user satisfaction of the human-computer interface
- Organogenesis in a dish: Modeling development and disease using organoid technologies
- GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor
- featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
- limma powers differential expression analyses for RNA-sequencing and microarray studies
- STAR: ultrafast universal RNA-seq aligner
- Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
- Hepatogenic differentiation from human adipose-derived stem cells and application for mouse acute liver injury
- The Gene Expression Omnibus database
- CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq
- From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline
- A Comprehensive Mouse Transcriptomic BodyMap across 17 Tissues by RNA-seq
- fastp: an ultra-fast all-in-one FASTQ preprocessor
- Progress and potential in organoid research
- Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris
- ArrayExpress update – from bulk to single-cell expression data
- High-throughput single-cell transcriptomics on organoids.
Cited by
- Organoid Models and Next-Generation Sequencing for Bone Marrow and Related Disorders
- Organoid: Bridging the gap between basic research and clinical practice.
- DiSignAtlas: an atlas of human and mouse disease signatures based on bulk and single-cell transcriptomics
- Identification of an immune-related eRNA prognostic signature for clear cell renal cell carcinoma
- A systematic review on the culture methods and applications of 3D tumoroids for cancer research and personalized medicine
- OrgXenomics: an integrated proteomic knowledge base for patient-derived organoid and xenograft
- Advancing cancer research through organoid technology
- Advancing Glioblastoma Research with Innovative Brain Organoid-Based Models
- Organoids as predictive platforms: advancing disease modeling, therapeutic innovation, and drug delivery systems.
- scGeneBank: cross-species screening of functional gene sets at single-cell resolution
- Organoids: A New Frontier in Precision Medicine and Engineering
- Integrating polygenic signals and single-cell multiomics identifies cell-type-specific regulomes critical for immune- and aging-related diseases
- EPB41L family serves as a prognostic biomarker for kidney renal clear cell carcinoma
- Organoids revolutionizing precancer research.
- O RGANOID C OMPUTER V ISION : A S URVEY AND O UTLOOK
- iOrganoAssay to Connect Microscopy Images to Organoid Assays for Long-Term Monitoring
- Breast cancer organoids: a precision platform for modeling heterogeneity and advancing personalized therapy
- Ultrasound-responsive nanomaterials for precision therapy in tumor organoids
- Human organoids: Fit for drug discovery?
Related papers
- Generation of Complete Multi−Cell Type Lung Organoids From Human Embryonic and Patient‐Specific Induced Pluripotent Stem Cells for Infectious Disease Modeling and Therapeutics Validation
- Transcriptome-Guided Design of Physiological Multilineage Liver Organoids
- Embryonic, Organ and Other Tissue Specific Stem Cells: C-MET-MUTATED HUMAN INDUCED PLURIPOTENT STEM CELL (IPSC)-DERIVED CARDIAC ORGANOIDS: A NOVEL MODEL OF HYPERTROPHIC CARDIOMYOPATHY
- Production of kidney organoids arranged around single ureteric bud trees, and containing endogenous blood vessels, solely from embryonic stem cells
- Legal and Ethical Considerations of Brain Organoid Technology
- The Application of Brain Organoids: From Neuronal Development to Neurological Diseases
- Liver Organoids: Updates on Disease Modeling and Biomedical Applications
- Hepatic Differentiation of Mouse Embryonic Stem Cells and Induced Pluripotent Stem Cells During Organoid Formation in Hollow Fibers
- The research progress of human organoids and the prospects of application in stomatology
- Biological techniques: Kidney tissue grown from induced stem cells