GEO series

Induced neural progenitor specification from human pluripotent stem cells by a refined synthetic Notch platform

GSE294935 Homo sapiens (human) RNA-seq (gene expression) 16 samples Submitted 2025/05/08 Platform GPL34281

At a glance

RNA-seq (gene expression) · human · 16 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: 16 samples: 4 × WT (-)SHH vs 4 × WT (+)SHH vs 4 × SynNotch (-)GFP vs 4 × SynNotch (+)GFPGroups 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: Induced Neural Progenitor Specification from Human Pluripotent Stem Cells by a Refined Synthetic Notch PlatformACS synthetic biology · 2025

Summary (written by the submitters)

Historically, studying the development of brain and central nervous system (CNS) tissues has been challenging. Human pluripotent stem cell (hPSC) technology has allowed for in vitro reconstitution of relevant, early cell trajectories by using small molecules and recombinant proteins to guide differentiation of cells towards relevant brain and CNS phenotypes.

Read the full summary ↓

However, many of these protocols fail to recapitulate the cell-guided differentiation programs intrinsic to embryonic development, particularly the signaling centers that emerge within the neural tube during brain formation. Located on the ventral end of the neural tube, the floor plate acts as one such signaling center to pattern the dorsal/ventral axis by secreting the morphogen Sonic Hedgehog (SHH). Here, we present a method for cell-guided differentiation using the synthetic Notch (synNotch) receptor platform to regulate SHH production and subsequent cell fate specification. We show that the widely used configuration of the orthogonal synNotch ligand green fluorescent protein (GFP) mounted on a platelet derived growth factor receptor-b transmembrane chassis does not allow for robust artificial signaling in synNotch-hPSCs (“receivers”) co-cultured with ligand-presenting hPSCs (“senders”). We discovered that refined designs of membrane-bound GFP-ligand allows for efficient receptor activation in hPSC receivers. A variant of this enhanced synNotch system drives production of SHH in hPSC sender:hPSC receiver co-cultures and gives rise to floor plate-like cell types seen during neural tube development. This revised synNotch platform has the potential to pattern hPSC differentiation programs in synthetic morphogenesis studies designed to uncover key paradigms of human CNS development.

Published in

Induced Neural Progenitor Specification from Human Pluripotent Stem Cells by a Refined Synthetic Notch Platform

Hamann CA, Kjar A, Kim H et al. · ACS synthetic biology 2025 · PMID 40327355 · doi:10.1021/acssynbio.4c00742

This dataset

Open GSE294935 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 GSE294935_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 PRJNA1251685 and SRA study SRP579130. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40327355) ↗

Study design

4 × WT (-)SHH vs 4 × WT (+)SHH vs 4 × SynNotch (-)GFP vs 4 × SynNotch (+)GFP

Supports a between-group comparison across 16 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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

GSM8931573 WT (-)SHH 1 WT (-)SHH
GSM8931574 WT (-)SHH 2 WT (-)SHH
GSM8931576 WT (-)SHH 3 WT (-)SHH
GSM8931577 WT (-)SHH 4 WT (-)SHH
GSM8931578 WT (+)SHH 1 WT (+)SHH
GSM8931579 WT (+)SHH 2 WT (+)SHH
GSM8931580 WT (+)SHH 3 WT (+)SHH
GSM8931581 WT (+)SHH 4 WT (+)SHH
GSM8931582 SynNotch (-)GFP 1 SynNotch (-)GFP
GSM8931583 SynNotch (-)GFP 2 SynNotch (-)GFP
GSM8931584 SynNotch (-)GFP 3 SynNotch (-)GFP
GSM8931585 SynNotch (-)GFP 4 SynNotch (-)GFP
GSM8931587 SynNotch (+)GFP 1 SynNotch (+)GFP
GSM8931588 SynNotch (+)GFP 2 SynNotch (+)GFP
GSM8931589 SynNotch (+)GFP 3 SynNotch (+)GFP
GSM8931590 SynNotch (+)GFP 4 SynNotch (+)GFP

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