GEO series

Two parallel neural ectoderm populations contribute to the developing brain [RNA-seq]

GSE286147 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2025/01/10 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 18 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: 18 samples: 9 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.

Summary (written by the submitters)

Stem cell research strives to create diverse types of human brain cells. Given plentiful successes in converting human pluripotent stem cells (hPSCs) into forebrain and midbrain cells, here we focus on generating cells of the human hindbrain, a life-sustaining brain region. This is, in turn, predicated on a developmental roadmap of when and how brain progenitors diversify from one another.

Read the full summary ↓

In one model, a common brain progenitor can generate all brain regions. Here our studies of mouse embryos and hPSCs support a different model that as early as gastrulation, two parallel brain progenitors emerge simultaneously: anterior neural ectoderm (forebrain/midbrain progenitor) and posterior neural ectoderm (which forms most of the hindbrain). Expanding on classical studies, we suggest anterior and posterior neural ectoderm are already lineage-committed in vitro and cannot transdifferentiate. Anterior and posterior neural ectoderm have divergent chromatin landscapes, respectively foreshadowing their forebrain versus hindbrain potentials. We differentiated hPSCs into posterior neural ectoderm, and subsequently, hindbrain rhombomere 5/6-specific motor neurons. Anterior and posterior neural ectoderm thus represent two parallel developmental routes to generate forebrain/midbrain vs. hindbrain neurons. Finally, anterior and posterior ectoderm are likely conserved from vertebrates to hemichordates, intimating an ancient neural lineage bifurcation that predated chordates, with implications for nervous system evolution.

This dataset

Open GSE286147 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 GSE286147_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 PRJNA1208004 and SRA study SRP556143. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

9 conditions, mostly in duplicate

hPSC_RNA ×2 aNE_RNA ×2 aNE_T_RNA ×2 aNE_M_RNA ×2 aNE_H_RNA ×2 pNE_RNA ×2 pNE_T_RNA ×2 pNE_M_RNA ×2 +1 more

Supports a between-group comparison across 18 samples.

How we read this: 9 replicated groups read from 18 sample titles; they account for 18 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

GSM8718652 hPSC_RNA_1 hPSC_RNA
GSM8718653 hPSC_RNA_2 hPSC_RNA
GSM8718654 aNE_RNA_1 aNE_RNA
GSM8718655 aNE_RNA_2 aNE_RNA
GSM8718656 aNE_T_RNA_1 aNE_T_RNA
GSM8718657 aNE_T_RNA_2 aNE_T_RNA
GSM8718658 aNE_M_RNA_1 aNE_M_RNA
GSM8718659 aNE_M_RNA_2 aNE_M_RNA
GSM8718660 aNE_H_RNA_1 aNE_H_RNA
GSM8718661 aNE_H_RNA_2 aNE_H_RNA
GSM8718662 pNE_RNA_1 pNE_RNA
GSM8718663 pNE_RNA_2 pNE_RNA
GSM8718664 pNE_T_RNA_1 pNE_T_RNA
GSM8718665 pNE_T_RNA_2 pNE_T_RNA
GSM8718666 pNE_M_RNA_1 pNE_M_RNA
GSM8718667 pNE_M_RNA_2 pNE_M_RNA
GSM8718668 pNE_H_RNA_1 pNE_H_RNA
GSM8718669 pNE_H_RNA_2 pNE_H_RNA

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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.