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Reconstitution of Human Brain Cell Diversity in Organoids via Four Protocols [time-course bulk RNA-seq]

GSE277967 Homo sapiens (human) RNA-seq (gene expression) 768 samples Submitted 2024/11/20 Platform GPL18573Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 768 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Samples
768 samples: 200 conditions, mostly in duplicateGroups 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
Quantitative profiling of human brain organoid cell diversity across four protocols and multiple cell linesCell reports · 2025
Summary (written by the submitters)
Systematic analysis of the cellular and transcriptional landscape of brain organoids grown from multiple cell lines using four different protocols recapitulating dorsal and ventral forebrain, midbrain, and striatum via time-course bulk-RNA sequencing.
Published in
Quantitative profiling of human brain organoid cell diversity across four protocols and multiple cell lines
Naas J, Balmaña M, Holcik L et al. · Cell reports 2025 · PMID 40864552 · doi:10.1016/j.celrep.2025.116168
This dataset
Open GSE277967 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 GSE277967_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1164907. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40864552) ↗
Study design
200 conditions, mostly in duplicate
176, D, day 13, biol repl 1, ×2 176, D, day 25, biol repl 1, ×2 176, D, day 40, biol repl 1, ×2 176, D, day 80, biol repl 1, ×2 176, D, day 120, biol repl 1, ×2 176, M, day 16, biol repl 1, ×2 176, M, day 40, biol repl 1, ×2 176, M, day 80, biol repl 1, ×2 +192 more

Supports a between-group comparison across 400 samples.

How we read this: 200 replicated groups read from the first 400 of 768 sample titles; they account for 400 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

+ 728 more — browse all 768 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

Share this dataset

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.