GEO series

Human liver sinusoidal endothelial cells support the development of functional human pluripotent stem cell-derived Kupffer cells

GSE250618 Homo sapiens (human) Single-cell RNA-seq 1 samples Submitted 2024/08/09 Platform GPL25526

At a glance

Single-cell RNA-seq · human · 1 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Homo sapiens (human)
Samples: 1 samples
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: Human liver sinusoidal endothelial cells support the development of functional human pluripotent stem cell-derived Kupffer cellsCell reports · 2024

Summary (written by the submitters)

In mice, Kupffer cells (KCs) first derive from yolk sac (YS) hematopoietic progenitors prior to the emergence of the hematopoietic stem cell. To investigate human KC ontogeny, we recapitulated YS hematopoiesis from human pluripotent stem cells (hPSCs) and transplanted derivative macrophage progenitors into NSG mice previously humanized with hPSC-liver sinusoidal endothelial cells (LSECs).

Read the full summary ↓

We demonstrate that hPSC-LSECs facilitate stable hPSC-YS-macrophage engraftment for at least 7 weeks. Single cell RNA sequencing of engrafted YS-macrophages revealed a homogenous MARCO-expressing KC gene signature and low expression of inflammatory macrophage genes. In contrast, human cord blood (CB)-derived macrophages generated grafts that contain multiple hematopoietic lineages in addition to KCs. Functional analyses showed that the engrafted KCs actively perform phagocytosis and erythrophagocytosis in vivo. Taken together, these findings demonstrate that it is possible to generate human KCs from hPSCs and show that the equivalent of the human YS hematopoietic programs represent enriched sources of progenitors for this lineage.

Published in

Human liver sinusoidal endothelial cells support the development of functional human pluripotent stem cell-derived Kupffer cells

Kent GM, Atkins MH, Lung B et al. · Cell reports 2024 · PMID 39146183 · doi:10.1016/j.celrep.2024.114629

This dataset

Open GSE250618 in finder → Find more 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 GSE250618_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 PRJNA1054627 and SRA study SRP478978. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39146183) ↗

Samples in this study

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+ 1 more — browse all 1 samples with per-sample file links →

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