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Spatiotemporal Analysis of Human Intestinal Development at Single Cell Resolution - Spatial Transcriptomics

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Dataset overview

Participants None
Samples 8
Reuse readiness 5.4/10 evidence-backed score

Spatiotemporal analysis of human intestinal development at single-cell resolution.

Fawkner-Corbett D, Antanaviciute A, Parikh K, Jagielowicz M, Gerós AS, Gupta T, Ashley N, Khamis D, et al. · Cell · 2021

Abstract

Development of the human intestine is not well understood. Here, we link single-cell RNA sequencing and spatial transcriptomics to characterize intestinal morphogenesis through time. We identify 101 cell states including epithelial and mesenchymal progenitor populations and programs linked to key morphogenetic milestones. We describe principles of crypt-villus axis formation; neural, vascular, mesenchymal morphogenesis, and immune population of the developing gut. We identify the differentiation hierarchies of developing fibroblast and myofibroblast subtypes and describe diverse functions for these including as vascular niche cells. We pinpoint the origins of Peyer's patches and gut-associated lymphoid tissue (GALT) and describe location-specific immune programs. We use our resource to present an unbiased analysis of morphogen gradients that direct sequential waves of cellular differentiation and define cells and locations linked to rare developmental intestinal disorders. We compile a publicly available online resource, spatio-temporal analysis resource of fetal intestinal development (STAR-FINDer), to facilitate further work.

doi:10.1016/j.cell.2020.12.016 ↗ PMID 33406409 ↗ PMC7864098 ↗

Study facts

Organism
Homo sapiens
Platform
10x Genomics Visium Spatial Gene Expression
Age group
mixed
Disease groups
—
Anatomical sites
colon tissue, whole colon section, whole small intestine section

Data availability

  • Raw counts
  • Processed matrix
  • Spatial coordinates
  • Histology images

File types TAR

Strengths & limitations for reuse

Strengths

  • Raw counts are advertised
  • Processed matrices are advertised
  • Spatial coordinates are advertised
  • Histology images are advertised

Limitations

  • 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.number_of_cells_or_spots 9330
This generated a dataset of 9330 tissue-covered spots with an average of 2480 genes detected per spot in each slide

Section Spatial transcriptomics, offset 106420
assay.platform 10x Genomics Visium Spatial Gene Expression
fetal and adult samples were then processed for full ST experiment as per manufacturer’s instructions (10x Genomics, Visium Spatial, Rev B)

Section Spatial transcriptomics, offset 104900
assay.platform_version Visium Spatial Rev B
10x Genomics, Visium Spatial, Rev B

Section Spatial transcriptomics, offset 104980
assay.reference_genome hg38 from source
hg38

Section GEO family SOFT, offset —
assay.resolution spot
Each spot covered a 55μm area with a 100μm center-to-center distance

Section Spatial transcriptomics, offset 106650
assay.sequencing_based True from source
GEO assay type/library strategy: RNA-SEQ

Section GEO family SOFT, offset —
assay.whole_transcriptome True from source
GEO library strategy=['RNA-SEQ']

Section GEO family SOFT, offset —

Cohort

FieldValueEvidence
cohort.age_group mixed
Colon and terminal ileum tissue sections from adult and fetal (12 and 19 post-conceptual weeks) were subject to spatial transcriptomics analysis

Section series_overall_design, offset 9500

Data_Assets

FieldValueEvidence
data_assets.file_manifest True from source
Supplementary files enumerated in family SOFT ()

Section GEO family SOFT, offset —
data_assets.histology_images True
spatial transcriptomics slide H&E image in jpeg format

Section data_processing, offset 11100
data_assets.open_access True
"license": "cc by"

Section publication metadata, offset —
data_assets.processed_matrix True
Spaceranger outputs - raw feature barcode matrix in mtx format, gene list in tab delimited format

Section data_processing, offset 11000
data_assets.raw_counts True
Spaceranger outputs - raw feature barcode matrix in mtx format

Section data_processing, offset 11000
data_assets.spatial_coordinates True
spot position to image pixel coordinates

Section data_processing, offset 11200

Specimens

FieldValueEvidence
specimens.anatomical_sites ['colon tissue', 'whole colon section', 'whole small intestine section'] from source
GEO sample source names: colon tissue; whole colon section; whole small intestine section

Section GEO family SOFT, offset —
specimens.number_of_samples 8 computed
8 GSM records parsed from GEO family SOFT

Section GEO family SOFT, offset —
specimens.preservation_method Freshly frozen in OCT blocks
adult and fetal intestinal samples were freshley frozen in OCT blocks and then sectioned onto an oligo-covered array

Section sample_characteristics, offset 10300