GEO series

The gene expression profiles of complete hydatidiform mole which developed post molar gestational trophoblast neoplasia

GSE252906 Homo sapiens (human) RNA-seq (gene expression) 13 samples Submitted 2024/12/21 Platform GPL28038

At a glance

RNA-seq (gene expression) · human · 13 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: 13 samples: 13 samples, each with a distinct title — no replicated groupsGroups 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: Elucidation of the role of XBP1 in the progression of complete hydatidiform mole to invasive mole through RNA-seqGynecologic oncology · 2024

Summary (written by the submitters)

A complete hydatidiform mole (CHM) is a common disease known to develop post-molar gestational trophoblast neoplasia (GTN). However, the details of the molecular biological mechanisms underlying the progression to post-molar GTN from hydatidiform moles are still largely unknown. In this study, we performed RNA sequencing (RNA-seq) using archival fresh frozen tissues of patients with CHM and compared the gene expression profiles of patients who achieved spontaneous remission and those who developed post-molar GTN after the evacuation.

Published in

Elucidation of the role of XBP1 in the progression of complete hydatidiform mole to invasive mole through RNA-seq

Shibata M, Yoshida K, Yokoi A et al. · Gynecologic oncology 2024 · PMID 39216132 · doi:10.1016/j.ygyno.2024.08.023

This dataset

Open GSE252906 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 GSE252906_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 PRJNA1063208 and SRA study SRP482895. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39216132) ↗

Study design

13 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 13 sample titles: 13 distinct titles with little repetition. 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

GSM8010117 CHM1, control
GSM8010118 CHM2, control
GSM8010119 CHM3, control
GSM8010120 CHM4, control
GSM8010121 CHM5, control
GSM8010122 CHM6, control
GSM8010123 CHM7, control
GSM8010124 CHM8, low-risk GTN
GSM8010125 CHM9, low-risk GTN
GSM8010126 CHM10, low-risk GTN
GSM8010127 CHM11, low-risk GTN
GSM8010128 CHM12, low-risk GTN
GSM8010129 CHM13, low-risk GTN

Datasets on a similar topic

GSE252907 Gene expression profiles of complete hydatidiform moles and XBP1-overexpressing cell lines associated with progression to gestational trophoblastic tumors 25 samples shares hydatidiform, gestational, trophoblast, profiles, complete
GSE328024 A multi-omic dataset of cellular and microRNA profiles in human breast milk across a spectrum of gestational ages 14 samples shares gestational, profiles
GSE237732 miR-146b-5p downregulates IRAK1 and ADAM19 to suppress trophoblast proliferation, invasion and migration in miscarriage [circRNA, lincRNA, and mRNA profiles] 10 samples shares trophoblast, profiles
GSE288317 JAX Study 1 and Study 2 - RNA-seq of male KOLF2.2J hiPSC-derived trophoblast cell lines homozygous null for 14 different transcription factors 172 samples shares trophoblast
GSE243579 iPSC-based modeling of preeclampsia identifies defects in extravillous trophoblast differentiation 144 samples shares trophoblast
GSE268230 Extracellular vesicles alter trophoblast function in pregnancies complicated by COVID-19 129 samples shares trophoblast
GSE221617 Leveraging chorionic villus biopsies for the derivation of patient-specific trophoblast stem cells 105 samples shares trophoblast
GSE288288 JAX Study 1- RNA-seq of male KOLF2.2J hiPSC-derived trophoblast cell lines homozygous null for seven different transcription factors 90 samples shares trophoblast

Search all human RNA-seq datasets in GEO →

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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.