GEO series

scRNAseq of human blood, tonsil, lung and small intestine innate lymphoid cells

GSE240441 Homo sapiens (human) Single-cell RNA-seq 18 samples Submitted 2024/06/14 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 18 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Homo sapiens (human)
Samples: 18 samples: 13 distinct titles, 2 of them repeatedGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper: Diversity of group 1 innate lymphoid cells in human tissuesNature immunology · 2024

Summary (written by the submitters)

Group 1 innate lymphoid cells (ILC1s) are cytotoxic and interferon gamma-producing lymphocytes lacking antigen-specific receptors, which include ILC1s and natural killer (NK) cells. In mice, ILC1s differ from NK cells, as they develop independently of the NK-specifying transcription factor EOMES, while requiring the repressor ZFP683 (ZNF683 in humans) for tissue residency.

Read the full summary ↓

Here we identify highly variable ILC1 subtypes across tissues through investigation of human ILC1 diversity by single-cell RNA sequencing and flow cytometry. The intestinal epithelium contained abundant mature EOMES− ILC1s expressing PRDM1 rather than ZNF683, alongside a few immature TCF7+PRDM1− ILC1s. Other tissues harbored NK cells expressing ZNF683 and EOMES transcripts; however, EOMES protein content was variable. These ZNF683+ NK cells are tissue-imprinted NK cells phenotypically resembling ILC1s. The tissue ILC1-NK spectrum also encompassed conventional NK cells and NK cells distinguished by PTGDS expression. These findings establish a foundation for evaluating phenotypic and functional changes within the NK-ILC1 spectrum in diseases.

Published in

Diversity of group 1 innate lymphoid cells in human tissues

Jaeger N, Antonova AU, Kreisel D et al. · Nature immunology 2024 · PMID 38956380 · doi:10.1038/s41590-024-01885-y

This dataset

Open GSE240441 in finder → Find more human RNA-seq datasets →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE240441_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1003807 and SRA study SRP454227. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38956380) ↗

Study design

13 distinct titles, 2 of them repeated

Tonsil ×5 Blood ×2

Supports a case/control comparison: 1 samples read as cases, 6 as controls.

How we read this: Read from 18 sample titles: 13 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM7698011 Blood 1
GSM7698012 Blood 2
GSM7698013 Tonsil 1
GSM7698014 Tonsil 2
GSM7698015 Tonsil 3
GSM7698016 Tonsil 4
GSM7698017 Tonsil 5
GSM7698018 N-1425-2 IEL 1, control ileum
GSM7698019 CD-1818-2 IEL 2,Crohn's disease, pooled non-inflamed and inflamed ileum
GSM7698020 N-1234 NKp44+ IEL 1, control ileum
GSM7698021 N-7420 NKp44+ IEL 2, control ileum
GSM7698022 N1425-4 LPL 1, control ileum
GSM7698023 Lung 1, control, donor
GSM7698024 Lung 2, fibrotic, recipient
GSM7698025 Lung 3, control, donor
GSM7698026 Lung 4, fibrotic, recipient
GSM8239723 Tonsils and PBMC NK cells, GEX
GSM8239724 Tonsils and PBMC NK cells, HTO

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