Foundry120 atlas

← IBD single-cell transcriptomics

Total - Cells of the human intestinal tract mapped across space and time

Download from source ↗

Dataset overview

Participants None
Samples 164
Reuse readiness 7.9/10 evidence-backed score

Cells of the human intestinal tract mapped across space and time.

Elmentaite R, Kumasaka N, Roberts K, Fleming A, Dann E, King HW, Kleshchevnikov V, Dabrowska M, et al. · Nature · 2021

Abstract

The cellular landscape of the human intestinal tract is dynamic throughout life, developing in utero and changing in response to functional requirements and environmental exposures. Here, to comprehensively map cell lineages, we use single-cell RNA sequencing and antigen receptor analysis of almost half a million cells from up to 5 anatomical regions in the developing and up to 11 distinct anatomical regions in the healthy paediatric and adult human gut. This reveals the existence of transcriptionally distinct BEST4 epithelial cells throughout the human intestinal tract. Furthermore, we implicate IgG sensing as a function of intestinal tuft cells. We describe neural cell populations in the developing enteric nervous system, and predict cell-type-specific expression of genes associated with Hirschsprung's disease. Finally, using a systems approach, we identify key cell players that drive the formation of secondary lymphoid tissue in early human development. We show that these programs are adopted in inflammatory bowel disease to recruit and retain immune cells at the site of inflammation. This catalogue of intestinal cells will provide new insights into cellular programs in development, homeostasis and disease.

doi:10.1038/s41586-021-03852-1 ↗ PMID 34497389 ↗ PMC8426186 ↗

Study facts

Organism
Homo sapiens
Platform
10x Genomics Chromium
Age group
mixed
Disease groups
—
Anatomical sites
cecum mucosa, colonic mucosa, duodenal mucosa, ileal mucosa, jejunal mucosa, mesenteric lymph node, mucosa of appendix, mucosa of ascending colon, mucosa of descending colon, mucosa of rectum, mucosa of sigmoid colon, mucosa of transverse colon

Data availability

  • Processed matrix

File types H5AD

Strengths & limitations for reuse

Strengths

  • Raw reads are advertised
  • Processed matrices are advertised
  • Cell metadata are advertised
  • Participant mapping is available

Limitations

  • Not documented: raw counts 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 10x 3' v2 from source
assay=10x 3' v2

Section structured repository metadata, offset —
assay.library_chemistry 10x Genomics 5′ gene expression v2 and 3′ gene expression v2
Chromium Single Cell 5′ gene expression v.2 (10x Genomics)

Section 10x Genomics Chromium GEX library preparation and sequencing, offset —
assay.platform 10x Genomics Chromium
loaded for droplet-based scRNA-seq according to the manufacturer’s protocol for the Chromium

Section 10x Genomics Chromium GEX library preparation and sequencing, offset —
assay.reference_genome GRCh38-3.0.0
the 10X human transcriptome GRCh38-3.0.0 as the reference

Section Pre-processing of 10x Genomics scRNA-seq data, offset —
assay.sequencing_type scrna_seq from source
sequencing_type=scrna_seq

Section structured repository metadata, offset —

Cohort

FieldValueEvidence
cohort.age_group mixed
in utero development, childhood and adulthood

Section Main, offset —

Data_Assets

FieldValueEvidence
data_assets.cell_metadata True from source
CELLxGENE dataset exposes cell metadata

Section structured repository metadata, offset —
data_assets.open_access True from source
public CELLxGENE dataset

Section structured repository metadata, offset —
data_assets.participant_metadata True from source
"donor_id": ["T036", "T110", "T161", "T057", "T182", "T044", "T024", "T197", "T160", "T176", "T019", "T202", "T017", "T189", "T203", "A32 (411C)", "A34 (417C)", "A39 (440C)", "A38 (432C)", "A26 (386C)", "F72", "F73", "F78", "F66", "F67", "BRC2258", "BRC2259", "BRC2029", "BRC2026", "BRC2043", "BRC2046", "BRC2049", "BRC2121", "BRC2119", "BRC2133", "BRC2134", "A33 (414C)", "A30 (398B)"]

Section —, offset —
data_assets.processed_matrix True from source
CELLxGENE dataset exposes H5AD

Section structured repository metadata, offset —
data_assets.raw_reads True from source
"link_type": "RAW_DATA"

Section —, offset —

Processing

FieldValueEvidence
processing.ambient_rna_correction_reported True
we apply the SoupX algorithm 50 with default parameters and function adjustCounts() to remove ambient mRNA from the count matrix

Section scRNA-seq quality control and processing of 10x sequencing data, offset —
processing.batch_correction_reported True
Batch correction of fetal and adult datasets was performed with bbknn

Section Cell-type annotation, offset —
processing.cell_type_annotation_method Marker-gene expression with Leiden clustering
cell lineages were annotated on the basis of algorithmically defined marker gene expression for each cluster

Section Cell-type annotation, offset —
processing.doublet_detection_reported True
A Scrublet (v.0.2.1) score cut-off of 0.25 was applied to assist with doublet exclusion

Section scRNA-seq quality control and processing of 10x sequencing data, offset —
processing.normalization_method Per-cell normalization and log transformation
Gene expression for each cell was normalized and log-transformed

Section scRNA-seq quality control and processing of 10x sequencing data, offset —
processing.quality_control_reported True
Cells for each dataset were filtered for more than 500 genes and less than 50% mitochondrial reads

Section scRNA-seq quality control and processing of 10x sequencing data, offset —

Specimens

FieldValueEvidence
specimens.anatomical_sites ['cecum mucosa', 'colonic mucosa', 'duodenal mucosa', 'ileal mucosa', 'jejunal mucosa', 'mesenteric lymph node', 'mucosa of appendix', 'mucosa of ascending colon', 'mucosa of descending colon', 'mucosa of rectum', 'mucosa of sigmoid colon', 'mucosa of transverse colon'] from source
tissues=cecum mucosa, colonic mucosa, duodenal mucosa, ileal mucosa, jejunal mucosa, mesenteric lymph node, mucosa of appendix, mucosa of ascending colon, mucosa of descending colon, mucosa of rectum, mucosa of sigmoid colon, mucosa of transverse colon

Section structured repository metadata, offset —
specimens.number_of_cells 428469 from source
cell_count=428469

Section structured repository metadata, offset —
specimens.number_of_samples 164
164 10x Genomics scRNAseq data and 3 10x Visium samples described in this study

Section Supplementary information, offset —
specimens.participant_to_sample_mapping_available True from source
"donor_id": ["T036", "T110", "T161", "T057", "T182", "T044", "T024", "T197", "T160", "T176", "T019", "T202", "T017", "T189", "T203", "A32 (411C)", "A34 (417C)", "A39 (440C)", "A38 (432C)", "A26 (386C)", "F72", "F73", "F78", "F66", "F67", "BRC2258", "BRC2259", "BRC2029", "BRC2026", "BRC2043", "BRC2046", "BRC2049", "BRC2121", "BRC2119", "BRC2133", "BRC2134", "A33 (414C)", "A30 (398B)"]

Section —, offset —