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On-chip neural induction boosts neural stem cell commitment: toward a pipeline for iPSC-based therapies

GSE255748 Homo sapiens (human) RNA-seq (gene expression) 26 samples Submitted 2024/04/08 Platform GPL30173
At a glance

RNA-seq (gene expression) · human · 26 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
26 samples: 8 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
On-Chip Neural Induction Boosts Neural Stem Cell Commitment: Toward a Pipeline for iPSC-Based TherapiesAdvanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024
Summary (written by the submitters)
The clinical translation of induced pluripotent stem cells (iPSCs) holds great potential for personalized therapeutics. However, the current workflow to generate iPSCs is expensive, time-consuming, and requires standardization. We present a simplified microfluidic approach for reprogramming fibroblasts into iPSCs and their subsequent differentiation into neural stem cells (NSCs).
Read the full summary ↓
Our method exploits microphysiological technology, providing a 100-fold reduction in reagents for reprogramming and a 9-fold reduction in number of input cells. The iPSCs generated from microfluidic reprogramming of fibroblasts show upregulation of pluripotency markers and downregulation of fibroblast markers, on par with those reprogrammed in the standardized well-conditions. The NSCs differentiated in microfluidic chips show upregulation of neuroectodermal markers (ZIC1, PAX6, SOX1), highlighting their propensity for nervous system development. We then compare the cells obtained on conventional well plates and microfluidic chips for reprogramming and neural induction by bulk RNA sequencing. Pathway enrichment analysis of NSCs generated in the chip showed neural stem cell development enrichment and boosted commitment to the neural stem cell lineage in the initial phases of neural induction, attributed to the confined environment in a microfluidic chip. This method provides a cost-effective pipeline to reprogram and differentiate iPSCs which can be made compliant with the current good manufacturing practices for therapeutics.
Published in
On-Chip Neural Induction Boosts Neural Stem Cell Commitment: Toward a Pipeline for iPSC-Based Therapies
Jain S, Voulgaris D, Thongkorn S et al. · Advanced science (Weinheim, Baden-Wurttemberg, Germany) 2024 · PMID 38655836 · doi:10.1002/advs.202401859
This dataset
Open GSE255748 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 GSE255748_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 PRJNA1076265 and SRA study SRP489590. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38655836) ↗
Study design
8 conditions, mostly in duplicate
iPS_C ×3 NSC_C9_well_p ×2 NSC_C9_chip_p ×2 NSC_C5_well_p ×2 NSC_C5_chip_p ×2 NSC_KTH_01_well_p ×2 NSC_KTH_01_chip_p ×2 NES_C ×2 +9 more

Supports a between-group comparison across 17 samples.

How we read this: 8 replicated groups read from 26 sample titles; they account for 17 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
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