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Transcriptomic analysis reveals the heterogeneous role of conducting films upon electrical stimulation

GSE261580 Homo sapiens (human) RNA-seq (gene expression) 16 samples Submitted 2024/09/05 Platform GPL20795
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: 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
Transcriptomic Analysis Reveals the Heterogeneous Role of Conducting Films Upon Electrical StimulationAdvanced healthcare materials · 2024
Summary (written by the submitters)
Central nervous system (CNS) injuries and neurodegenerative diseases have markedly poor prognoses and can result in permanent dysfunction due to the general inability of CNS neurons to regenerate. Differentiation of transplanted stem cells has emerged as a therapeutic avenue to regenerate tissue architecture in damaged areas. Electrical stimulation is a promising approach for directing the differentiation outcomes and pattern of outgrowth of transplanted stem cells, however traditional inorganic bio-electrodes can induce adverse effects such as inflammation.
Read the full summary ↓
Here, we demonstrate the implementation of two organic thin films, a polymer/reduced graphene oxide nanocomposite (P(rGO)) and PEDOT:PSS, that have favorable properties for implementation as conductive materials for electrical stimulation, as well as an inorganic indium tin oxide (ITO) conductive film. Transcriptomic analysis revealed that electrical stimulation improved neuronal differentiation of SH-SY5Y cells on all three films, with the greatest effect for P(rGO). Unique material- and electrical stimuli-mediated effects were observed, associated with differentiation, cell-substrate adhesion, and translation. Our work demonstrates that P(rGO) and PEDOT:PSS are highly promising organic materials for the development of biocompatible, conductive scaffolds that will enhance electrically-aided stem cell therapeutics for CNS injuries and neurodegenerative diseases.
Published in
Transcriptomic Analysis Reveals the Heterogeneous Role of Conducting Films Upon Electrical Stimulation
Lawler NB, Bhatt U, Agarwal V et al. · Advanced healthcare materials 2024 · PMID 39221662 · doi:10.1002/adhm.202400364
This dataset
Open GSE261580 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 GSE261580_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 PRJNA1087729 and SRA study SRP495231. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39221662) ↗
Study design
8 conditions, mostly in duplicate
Untreated control, ×2 Differentiated control, ×2 P(rGO) with electrical stimulation, ×2 P(rGO) no electrical stimulation, ×2 ITO with electrical stimulation, ×2 ITO no electrical stimulation, ×2 PSS with electrical stimulation, ×2 PSS no electrical stimulation, ×2

Supports a between-group comparison across 16 samples.

How we read this: 8 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
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