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Unveiling Tissue-Specific Transcriptional Adaptations in iPSC-Derived Fibroblasts via Co-Culture Systems

GSE294057 Homo sapiens (human) RNA-seq (gene expression) 27 samples Submitted 2025/07/07 Platform GPL34281
At a glance

RNA-seq (gene expression) · human · 27 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
27 samples: 9 conditions, mostly in triplicateGroups 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)
Induced pluripotent stem cell-derived fibroblasts (iFBs) are promising tools for autologous disease modelling, but their ability to replicate tissue-specific fibroblast characteristics remains unclear. Fibroblasts are highly heterogeneous, with distinct subtypes playing critical roles in tissue function and organ integrity.
Read the full summary ↓
This study investigates whether iFBs can acquire tissue-specific transcriptional profiles through co-culture with cells found in the skin (keratinocytes), heart (cardiomyocytes), gut (intestinal) and lung (bronchial epithelial Transcriptomic analyses revealed that iFBs exhibit transcriptional plasticity, adopting molecular phenotypes aligned with their co-culture environment across all three germ layers.Additionally, paracrine signalling induced tissue-specific changes in indirectly co-cultured iFBs, though these adaptations were transient without sustained interaction.These findings demonstrate the potential of iFBs to mimic native fibroblast behaviour but also highlight the need for validation in complex tissue models to account for variability in iPSC differentiation and functional stability. By providing evidence of tissue-specific plasticity, this study supports the utility of iFBs in developing physiologically relevant in vitro systems.
This dataset
Open GSE294057 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 GSE294057_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 PRJNA1247969 and SRA study SRP577239. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
9 conditions, mostly in triplicate
induced pluripotent stem cell-derived fibrobl… ×3 induced pluripotent stem cell-derived fibrobl… ×3 induced pluripotent stem cell-derived fibrobl… ×3 induced pluripotent stem cell-derived fibrobl… ×3 induced pluripotent stem cell-derived fibrobl… ×3 induced pluripotent stem cell-derived fibrobl… ×3 induced pluripotent stem cell-derived fibrobl… ×3 induced pluripotent stem cell-derived fibrobl… ×3 +1 more

Supports a between-group comparison across 27 samples.

How we read this: 9 replicated groups read from 27 sample titles; they account for 27 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
Datasets on a similar topic

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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.