GEO series

Single-cell atlas of the human brain vasculature across development, adulthood and disease (scRNA-Seq)

GSE256490 Homo sapiens (human) Single-cell RNA-seq 71 samples Submitted 2024/02/29 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 71 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: 71 samples: 69 distinct titles, 1 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: Single-cell atlas of the human brain vasculature across development, adulthood and diseaseNature · 2024

Summary (written by the submitters)

A broad range of brain pathologies critically relies on the vasculature, and cerebrovascular disease is a leading cause of death worldwide. However, the cellular and molecular architecture of the human brain vasculature remains incompletely understood. Here, we performed single-cell RNA sequencing of 606,380 freshly isolated endothelial, perivascular and other tissue-derived cells from 117 samples, from 68 human fetuses and adult patients to construct a molecular atlas of the developing fetal, adult control and diseased human brain vasculature.

Read the full summary ↓

We uncover extensive molecular heterogeneity of the vasculature of healthy fetal and adult human brains and across eight vascular-dependent Central Nervous System (CNS) pathologies including brain tumors and brain vascular malformations. We identify alteration of arteriovenous differentiation and reactivated fetal as well as conserved dysregulated genes and pathways in the diseased vasculature. Pathological endothelial cells display a loss of CNS-specific properties and reveal an upregulation of MHC class II molecules, indicating atypical features of CNS endothelial cells. Cell-cell interaction analyses predict numerous endothelial-to-perivascular cell ligand-receptor crosstalk including immune-related and angiogenic pathways, thereby unraveling a central role for the endothelium within brain neurovascular unit signaling networks. Our single-cell brain atlas provides insight into the molecular architecture and heterogeneity of the developing, adult/control and diseased human brain vasculature and serves as a powerful reference for future studies

Published in

Single-cell atlas of the human brain vasculature across development, adulthood and disease

Wälchli T, Ghobrial M, Schwab M et al. · Nature 2024 · PMID 38987604 · doi:10.1038/s41586-024-07493-y

This dataset

Open GSE256490 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 GSE256490_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 PRJNA800024 and SRA study SRP356459. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38987604) ↗

Study design

69 distinct titles, 1 of them repeated

TL_patient8_all cells ×3

How we read this: Read from 71 sample titles: 69 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

GSM8101522 FETAL_brain_IND1_EC
GSM8101523 FETAL_brain_IND2_IND3_EC
GSM8101524 FETAL_brain_IND4_EC
GSM8101525 FETAL_brain_IND5_EC
GSM8101526 FETAL_periphery_IND2_EC_kidney
GSM8101527 FETAL_periphery_IND3_EC_kidney
GSM8101528 FETAL_periphery_IND4_EC_leg
GSM8101529 FETAL_periphery_IND5_EC_throat
GSM8101530 FETAL_periphery_IND5_EC_kidney
GSM8101531 FETAL_periphery_IND5_EC_arm
GSM8101532 FETAL_periphery_IND5_EC_heart
GSM8101533 FETAL_periphery_IND6_EC_arm
GSM8101534 TL_patient1_EC
GSM8101535 TL_patient2_EC
GSM8101536 TL_patient3_EC
GSM8101537 TL_patient4_EC
GSM8101538 TL_patient5_EC
GSM8101539 TL_patient6_EC
GSM8101540 AVM_patient1_EC
GSM8101541 AVM_patient2_EC
GSM8101542 AVM_patient3_EC
GSM8101543 AVM_patient4_EC
GSM8101544 AVM_patient5_EC
GSM8101545 LGG_patient1_EC
GSM8101546 LGG_patient2_EC
GSM8101547 LGG_patient3_EC
GSM8101548 LGG_patient4_EC
GSM8101549 GBM_patient1_EC
GSM8101550 GBM_patient2_EC
GSM8101551 GBM_patient3_EC
GSM8101552 GBM_patient4_EC
GSM8101553 GBM_patient5_EC
GSM8101554 MET_patient1_EC
GSM8101555 MET_patient2_EC
GSM8101556 MET_patient3_EC
GSM8101557 MET_patient4_EC
GSM8101558 MET_patient5_EC
GSM8101559 MEN_patient1_EC
GSM8101560 MEN_patient2_EC
GSM8101561 MEN_patient3_EC

+ 31 more — browse all 71 samples with per-sample file links →

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Search all human RNA-seq datasets in GEO →

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.