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Hypoxia and loss of GCM1 expression prevents differentiation and contact inhibition in human trophoblast stem cells [RNA-Seq 2]

GSE276594 Homo sapiens (human) RNA-seq (gene expression) 45 samples Submitted 2024/10/02 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 45 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
45 samples: 18 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
Hypoxia and loss of GCM1 expression prevents differentiation and contact inhibition in human trophoblast stem cellsbioRxiv : the preprint server for biology · 2024
Summary (written by the submitters)
The placenta develops alongside the embryo and nurtures fetal development to term. During the first stages of embryonic development, due to low blood circulation, the blood and ambient oxygen supply is normally very low (~1-2% O2) and gradually increases upon placental invasion. While a hypoxic environment is associated with stem cell self-renewal and proliferation, persistent hypoxia may have severe effects on differentiating cells and could be the underlying cause of placental disorders.
Read the full summary ↓
We find that human trophoblast stem cells (TSC) thrive in low oxygen, whereas differentiation of syncytiotrophoblast (STB) and extravillous trophoblast (EVT) is negatively affected by hypoxic conditions. We find that the pro-differentiation factor GCM1 (human Glial Cell Missing-1) is downregulated in low oxygen, and there is substantial reduction of GCM1-regulated genes in hypoxic conditions. Knock-out of GCM1 in TSC caused impaired EVT and STB formation and function, reduced expression of genes that respond to differentiation, and resulted in maintenance of self-renewal genes. Treatment with a PI3K inhibitor reported to reduce GCM1 protein levels likewise counteracts spontaneous or directed differentiation. Chromatin immunoprecipitation of GCM1 showed enrichment of GCM1-specific binding near key transcription factors upregulated upon differentiation including the contact inhibition factor CDKN1C. Loss of GCM1 resulted in downregulation of CDKN1C and corresponding loss of contact inhibition, implicating GCM1 in regulation of this critical process.
Published in
Hypoxia and loss of GCM1 expression prevents differentiation and contact inhibition in human trophoblast stem cells
Cinkornpumin JK, Kwon SY, Prandstetter AM et al. · bioRxiv : the preprint server for biology 2024 · PMID 39314437 · doi:10.1101/2024.09.10.612343
This dataset
Open GSE276594 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 GSE276594_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 PRJNA1157885 and SRA study SRP531177. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39314437) ↗
Study design
18 conditions, mostly in duplicate
CT3-EVT-non-target2_c ×3 CT3-STB3D-non-target2_c ×3 CT3-TSC-non-target2_c ×3 CT3-EVT-non-target_c1 ×2 CT3-EVT-GCM1KO1_c1 ×2 CT1-TSC-non-target_c1 ×2 CT1-TSC-GCM1KO1_c1 ×2 CT1-EVT-non-target_c1 ×2 +16 more

Supports a between-group comparison across 39 samples.

How we read this: 18 replicated groups read from 45 sample titles; they account for 39 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

+ 5 more — browse all 45 samples with per-sample file links →

Datasets on a similar topic

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