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Derivation of human trophoblast stem cells from placentas at birth

GSE267112 Homo sapiens (human) RNA-seq (gene expression) 17 samples Submitted 2024/05/09 Platform GPL20301
At a glance

RNA-seq (gene expression) · human · 17 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
17 samples: 6 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
Derivation of human trophoblast stem cells from placentas at birthThe Journal of biological chemistry · 2025
Summary (written by the submitters)
Human trophoblast stem cells (hTSCs) have emerged as a powerful tool for modeling the placental cytotrophoblast (CTB) in vitro. hTSCs were originally derived from CTBs of the first trimester or blastocyst-stage embryos in trophoblast stem cell medium (TSCM) that contains epidermal growth factor (EGF), the glycogen synthase kinase-beta (GSK3b) inhibitor CHIR99021, the transforming growth factor-beta (TGFb) inhibitors A83-01 and SB431542, valproic acid (VPA), and the Rho-associated protein kinase (ROCK) inhibitor Y27632.
Read the full summary ↓
Here we show that hTSCs can be derived from CTBs isolated from the term placenta, using TSCM supplemented with a low concentration of mitochondrial pyruvate uptake inhibitor UK5099 and lipid-rich albumin (TUA medium). Notably, hTSCs could not be derived from term CTBs using TSCM alone, or in the absence of either UK5099 or lipid-rich albumin. Strikingly, hTSCs cultured in TUA medium for a few passages could be transitioned into TSCM and cultured thereafter in TSCM. hTSCs from term CTBs cultured in TUA medium as well as those transitioned into and cultured in TSCM thereafter could be differentiated to the extravillous trophoblast and syncytiotrophoblast lineages, and exhibited high transcriptome similarity with hTSCs derived from first trimester CTBs. We anticipate that these results will enable facile derivation of hTSCs from normal and pathological placentas at birth with diverse genetic backgrounds, and facilitate in vitro mechanistic studies in trophoblast biology.
Published in
Derivation of human trophoblast stem cells from placentas at birth
Karakis V, Britt JW, Jabeen M et al. · The Journal of biological chemistry 2025 · PMID 40221000 · doi:10.1016/j.jbc.2025.108505
This dataset
Open GSE267112 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 GSE267112_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 PRJNA1107599 and SRA study SRP505968. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40221000) ↗
Study design
6 conditions, mostly in duplicate
RESUB-CTB21126R--TUA-p ×3 RESUB-CTB21126R--TSCMa-p ×3 RESUB-CTB22131R--TUA-p ×2 RESUB-CTB21126R--TSCM -p7 ×2 RESUB-CTB22131R--TSCM-fr-TUA-p9 ×2 RESUB-CTB22131R-TSCMa-p ×2 RESUB-CTB22131R+ TUA p12 v ×1 RESUB-CTB21126R--TSCM p7 ×1 +1 more

Supports a between-group comparison across 14 samples.

How we read this: 6 replicated groups read from 17 sample titles; they account for 14 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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