GEO series

Temporal Differences in Progenitor Metabolism Shape Regional Brain Growth during Development [scRNA-seq]

GSE290353 Homo sapiens (human) Single-cell RNA-seq 12 samples Submitted 2025/04/18 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 12 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: 12 samples: 6 × Neocortex DIV vs 6 × Hindbrain DIVGroups 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.

Summary (written by the submitters)

Mammalian brain development is characterized by disproportionate forebrain expansion, yet the mechanisms underlying this regional growth specificity remain poorly understood. Here, we provide a single-cell-resolution birthdate atlas of the mouse brain (www.neurobirth.org), which reveals that while hindbrain neurogenesis is transient and restricted to early development, forebrain neurogenesis is temporally sustained through reduced consumptive divisions of ventricular zone progenitors, maintaining its germinal pool.

Read the full summary ↓

This atlas additionally reveals region-specific patterns of direct and indirect neurogenesis. Using single-cell RNA sequencing, we identify evolutionarily conserved cell-cycle programs and metabolism-related molecular pathways that control regional temporal windows of proliferation. We identify the late forebrain-enriched mitochondrial protein Fam210b as a key regulator using in vivo gain- and loss-of-function experiments. Fam210b elongates mitochondria and increases lactate production, which promotes progenitor self-renewing divisions and, ultimately, larger clonal size of their progeny. Together, these findings indicate spatiotemporal heterogeneity in mitochondrial function regulates progenitor cycling behavior and regional neuronal production during brain development.

This dataset

Open GSE290353 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 GSE290353_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 PRJNA1227531 and SRA study SRP566004. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 × Neocortex DIV vs 6 × Hindbrain DIV

Supports a between-group comparison across 12 samples.

How we read this: 2 replicated groups read from 12 sample titles; they account for 12 of them. 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

GSM8811118 Neocortex DIV5 Neocortex DIV
GSM8811119 Hindbrain DIV5 Hindbrain DIV
GSM8811120 Neocortex DIV10 Neocortex DIV
GSM8811121 Hindbrain DIV10 Hindbrain DIV
GSM8811122 Neocortex DIV13 Neocortex DIV
GSM8811123 Hindbrain DIV13 Hindbrain DIV
GSM8811124 Neocortex DIV15 Neocortex DIV
GSM8811125 Hindbrain DIV15 Hindbrain DIV
GSM8811126 Neocortex DIV17 Neocortex DIV
GSM8811127 Hindbrain DIV17 Hindbrain DIV
GSM8811128 Neocortex DIV20 Neocortex DIV
GSM8811129 Hindbrain DIV20 Hindbrain DIV

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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.