← BioTransfer GEO Dataset Finder
GEO series

Leveraging chorionic villus biopsies for the derivation of patient-specific trophoblast stem cells

GSE221617 Homo sapiens (human) RNA-seq (gene expression) 105 samples Submitted 2025/06/10 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 105 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
105 samples: 35 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
Leveraging chorionic villus biopsies for the derivation of patient-specific trophoblast stem cellsCommunications biology · 2025
Summary (written by the submitters)
Human trophoblast stem (TS) cells are an informative in vitro model for the generation and testing of biologically meaningful hypotheses. The goal of this project was to derive patient-specific TS cell lines from clinically available chorionic villus sampling (CVS) biopsies. Cell outgrowths were captured from human CVS tissue specimens cultured in modified human TS cell medium.
Read the full summary ↓
Cell colonies emerged early during the culture and cell lines were established and passaged for several generations. Karyotypes of the newly established CVS-derived trophoblast stem (TSCV) cell lines were determined and compared to initial genetic diagnoses from freshly isolated chorionic villi. Phenotypes of TSCV cells in the stem state and following differentiation were compared to cytotrophoblast-derived TS (TSCT) cells. TSCV and TSCT cells uniformly exhibited similarities in the stem state and following differentiation into syncytiotrophoblast. These shared features included morphology and gene expression. TSCV cell differentiation into extravillous trophoblast cells exhibited cell line dependent phenotypes. CVS tissue specimens provide a valuable source for TS cell derivation. They expand the genetic diversity of available TS cells and are associated with defined clinical outcomes. TSCV cell lines provide a new set of experimental tools for investigating trophoblast cell lineage development.
Published in
Leveraging chorionic villus biopsies for the derivation of patient-specific trophoblast stem cells
Varberg KM, Moreno-Irusta A, Novoa A et al. · Communications biology 2025 · PMID 40596474 · doi:10.1038/s42003-025-08393-1
This dataset
Open GSE221617 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 GSE221617_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 PRJNA915083 and SRA study SRP414515. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40596474) ↗
Study design
35 conditions, mostly in triplicate
CT27_EVT_D3 ×3 CT27_EVT_prot1 ×3 CT27_EVT_D6 ×3 CT27_EVT_prot2 ×3 CT27_ST3D ×3 CT27_Stem ×3 CT29_EVT_prot1 ×3 CT29_EVT_prot2 ×3 +27 more

Supports a between-group comparison across 105 samples.

How we read this: 35 replicated groups read from 105 sample titles; they account for 105 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

+ 65 more — browse all 105 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

Share this dataset

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.