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Transcriptome analysis of HUVECs and those transduced with hiHepPC-inducing factors in culture with or without CHIR99021 [RNA-Seq]

GSE279106 Homo sapiens (human) RNA-seq (gene expression) 25 samples Submitted 2025/11/24 Platform GPL24676Platform GPL15520
At a glance

RNA-seq (gene expression) · human · 25 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
25 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.
Paper
Activation of canonical Wnt signaling is required for efficient direct reprogramming into human hepatic progenitor cellsStem cell reports · 2025
Summary (written by the submitters)
We previously showed that a specific combination of three transcription factors (FOXA3, HNF1A, and HNF6) can induce direct reprogramming of human umbilical vein endothelial cells (HUVECs) and peripheral blood-derived endothelial cells into human induced hepatic progenitor cells (hiHepPCs; PMID: 33087715). However, the low induction efficiency of hiHepPCs will be a problem when using them in research and clinical applications.
Read the full summary ↓
Here, we show that activation of the canonical Wnt signaling pathway increase the reprogramming efficiency of HUVECs to hiHepPCs by rapidly inducing chromatin remodeling and gene expression changes in the transduced HUVECs.
Published in
Activation of canonical Wnt signaling is required for efficient direct reprogramming into human hepatic progenitor cells
Miura S, Horisawa K, Inada H et al. · Stem cell reports 2025 · PMID 41173009 · doi:10.1016/j.stemcr.2025.102688
This dataset
Open GSE279106 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 GSE279106_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 PRJNA1170875 and SRA study SRP537371. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41173009) ↗
Study design
9 conditions, mostly in triplicate
HUVECs transduced with FOXA3, HNF1A and HNF6,… ×3 HUVECs transduced with FOXA3, HNF1A and HNF6,… ×3 HUVECs transduced with FOXA3, HNF1A and HNF6,… ×3 HUVECs transduced with FOXA3, HNF1A and HNF6,… ×3 HUVECs transduced with FOXA3, HNF1A and HNF6,… ×3 HUVECs transduced with FOXA3, HNF1A and HNF6,… ×3 HUVECs, Lot ×3 HUVECs transduced with FOXA3, HNF1A and HNF6,… ×2 +1 more

Supports a between-group comparison across 25 samples.

How we read this: 9 replicated groups read from 25 sample titles; they account for 25 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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