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Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing

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Dataset overview

Participants None
Samples 28
Reuse readiness 6.0/10 evidence-backed score

Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing.

Mazzurana L, Czarnewski P, Jonsson V, Wigge L, Ringnér M, Williams TC, Ravindran A, Björklund ÅK, et al. · Cell research · 2021

Abstract

The impact of the microenvironment on innate lymphoid cell (ILC)-mediated immunity in humans remains largely unknown. Here we used full-length Smart-seq2 single-cell RNA-sequencing to unravel tissue-specific transcriptional profiles and heterogeneity of CD127<sup>+</sup> ILCs across four human tissues. Correlation analysis identified gene modules characterizing the migratory properties of tonsil and blood ILCs, and signatures of tissue-residency, activation and modified metabolism in colon and lung ILCs. Trajectory analysis revealed potential differentiation pathways from circulating and tissue-resident naïve ILCs to a spectrum of mature ILC subsets. In the lung we identified both CRTH2<sup>+</sup> and CRTH2<sup>-</sup> ILC2 with lung-specific signatures, which could be recapitulated by alarmin-exposure of circulating ILC2. Finally, we describe unique TCR-V(D)J-rearrangement patterns of blood ILC1-like cells, revealing a subset of potentially immature ILCs with TCR-δ rearrangement. Our study provides a useful resource for in-depth understanding of ILC-mediated immunity in humans, with implications for disease.

doi:10.1038/s41422-020-00445-x ↗ PMID 33420427 ↗ PMC8089104 ↗

Study facts

Organism
Homo sapiens
Platform
Illumina HiSeq 2500; Illumina HiSeq 2000; Illumina NovaSeq 6000
Age group
—
Disease groups
—
Anatomical sites
blood, lung, ascending colon, tonsil

Data availability

  • Raw counts
  • Processed matrix

File types CSVTAR

Strengths & limitations for reuse

Strengths

  • Raw reads are advertised
  • Raw counts are advertised
  • Processed matrices are advertised
  • Cell metadata 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.assay_type Smart-seq2
Smart-Seq2

Section extract_protocol, offset —
assay.library_chemistry Smart-seq2
Sorted cells were processed using the Smart-seq2 protocol

Section extract_protocol, offset —
assay.platform Illumina HiSeq 2500; Illumina HiSeq 2000; Illumina NovaSeq 6000
"instrument_model": {"Illumina HiSeq 2500": 13, "Illumina HiSeq 2000": 12, "Illumina NovaSeq 6000": 3}

Section instrument_model, offset —
assay.reference_genome hg19 –GRCh38
The reads were aligned to the human genome (hg19 –GRCh38)

Section data_processing, offset —
assay.sequencing_type scrna_seq
Sorted cells were processed using the Smart-seq2 protocol

Section extract_protocol, offset —

Data_Assets

FieldValueEvidence
data_assets.cell_metadata True
GSE150050_all_cells_metadata_with_QC.csv.gz

Section filelist.txt, offset —
data_assets.open_access True
Public on Dec 14 2020

Section series_status, offset —
data_assets.processed_matrix True
GSE150050_filtered_cells_logTPM.csv.tar.gz

Section filelist.txt, offset —
data_assets.raw_counts True
GSE150050_all_cells_STAR_raw_counts.csv.tar.gz

Section filelist.txt, offset —
data_assets.raw_reads True
GSE150050_RAW.tar

Section filelist.txt, offset —

Processing

FieldValueEvidence
processing.normalization_method TPM normalization
GSE150050_all_cells_TPM_normalized.csv.tar.gz

Section filelist.txt, offset —
processing.quality_control_reported True
GSE150050_all_cells_metadata_with_QC.csv.gz

Section filelist.txt, offset —

Specimens

FieldValueEvidence
specimens.anatomical_sites ['blood', 'lung', 'ascending colon', 'tonsil']
peripheral blood from three healthy donors, lung tissue from four patients undergoing lobectomy for lung cancer, and biopsies from the ascending colon ... The previously published tonsil data was also used

Section series_overall_design, offset —
specimens.number_of_samples 28
"sample_count": 28

Section sample_count, offset —
specimens.specimen_type mixed
lung tissue from four patients undergoing lobectomy for lung cancer, and biopsies from the ascending colon

Section series_overall_design, offset —