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Geometric engineering of organoid culture for enhanced organogenesis in a dish

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Dataset overview

Participants None
Samples 5
Reuse readiness 5.7/10 evidence-backed score

Geometric engineering of organoid culture for enhanced organogenesis in a dish.

Park SE, Kang S, Paek J, Georgescu A, Chang J, Yi AY, Wilkins BJ, Karakasheva TA, et al. · Nature methods · 2022

Abstract

Here, we introduce a facile, scalable engineering approach to enable long-term development and maturation of organoids. We have redesigned the configuration of conventional organoid culture to develop a platform that converts single injections of stem cell suspensions to radial arrays of organoids that can be maintained for extended periods without the need for passaging. Using this system, we demonstrate accelerated production of intestinal organoids with significantly enhanced structural and functional maturity, and their continuous development for over 4 weeks. Furthermore, we present a patient-derived organoid model of inflammatory bowel disease (IBD) and its interrogation using single-cell RNA sequencing to demonstrate its ability to reproduce key pathological features of IBD. Finally, we describe the extension of our approach to engineer vascularized, perfusable human enteroids, which can be used to model innate immune responses in IBD. This work provides an immediately deployable platform technology toward engineering more realistic organ-like structures in a dish.

doi:10.1038/s41592-022-01643-8 ↗ PMID 36280722 ↗ PMC10027401 ↗

Study facts

Organism
Homo sapiens
Platform
Illumina NovaSeq 6000
Age group
—
Disease groups
—
Anatomical sites
terminal ileum

Data availability

  • Raw counts
  • Processed matrix

File types MTXTSV

Strengths & limitations for reuse

Strengths

  • Raw reads are advertised
  • Raw counts are advertised
  • Processed matrices are advertised

Limitations

  • Not documented: cell metadata are advertised
  • Not documented: participant counts are documented
Extraction evidence & provenance

Each extracted field is shown with the source excerpt and location used to resolve it.

Assay

FieldValueEvidence
assay.assay_type single-cell RNA sequencing
its interrogation using single-cell RNA sequencing

Section —, offset —
assay.library_chemistry Chromium 10X Genomics Single Cell 3’ Reagent Kit v2
Chromium 10X Genomics Single Cell 3’ Reagent Kit v2 library chip

Section sample_values_with_sample_counts, offset —
assay.platform Illumina NovaSeq 6000
"instrument_model": {"Illumina NovaSeq 6000": 5}

Section instrument_model, offset —
assay.reference_genome GRCh38
aligned to the human genome GRCh38 transcriptome

Section data_processing, offset —
assay.sequencing_type scrna_seq
Intestinal epithelial cells isolated from enteroids of the control and IBD patients were analyzed using scRNAseq.

Section series_overall_design, offset —

Cohort

FieldValueEvidence
cohort.treatment_exposure_documented True from source
GEO sample characteristics document treatment/therapy

Section GEO family SOFT, offset —

Data_Assets

FieldValueEvidence
data_assets.open_access True
"series_status": "Public on Jan 12 2023"

Section series, offset —
data_assets.processed_matrix True
Supplementary files format and content: barcodes, features, and matrix files

Section sample_values_with_sample_counts, offset —
data_assets.raw_counts True
Supplementary files format and content: barcodes, features, and matrix files

Section data_processing, offset —
data_assets.raw_reads True
GSE203380_RAW.tar

Section filelist.txt, offset —

Processing

FieldValueEvidence
processing.normalization_method normalized for sequencing depth across the sample set
libraries were normalized for sequencing depth across the sample set

Section sample_values_with_sample_counts, offset —
processing.quality_control_reported True
For initial filtering, cells with a smaller number (< 200) of uniquely detected genes were excluded.

Section data_processing, offset —

Specimens

FieldValueEvidence
specimens.anatomical_sites ['terminal ileum']
"source_name": {"terminal ileum": 5}

Section sample_values_with_sample_counts.source_name, offset —
specimens.number_of_samples 5
"sample_count": 5

Section geo_family_soft, offset —
specimens.specimen_type biopsy
Enteroid lines are generated from terminal ileum mucosal biopsies.

Section extract_protocol, offset —