← BioTransfer GEO Dataset Finder
GEO series

Effects of PFOA, PFBA, PFHxA, PFOS, PFBS, PFHxS on gene expression in monolayer and non-neuroectoderm cells differentiated from H1

GSE236956 Homo sapiens (human) RNA-seq (gene expression) 42 samples Submitted 2024/04/28 Platform GPL30209
At a glance

RNA-seq (gene expression) · human · 42 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
42 samples: 42 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
Understanding the effects of per- and polyfluoroalkyl substances on early skin development: Role of ciliogenesis inhibition and altered microtubule dynamicsThe Science of the total environment · 2024
Summary (written by the submitters)
Per- and polyfluoroalkyl substances (PFAS) are a group of organic chemicals that contain multiple carbon-fluorine bonds, which make them highly stable and widespread in our environment, even in the human body. They have been detected in cord blood and showed correlation with neonatal health abnormalities such as weight loss. Here, we utilized human embryonic stem cell-based model to assess the early developmental toxicity of six PFAS (PFOA, PFHxA, PFBA, PFOS, PFHxS, and PFBS) and their skin developmental toxicity.
Read the full summary ↓
We employed global monolayer differentiated model to mimic the early embryonic development and performed non-neural ectoderm (NNE) differentiation which can give rise to keratinocytes to imitate early skin development. Transcriptomic analysis revealed that PFOS caused the most differentially expressed genes (DEGs) both in day 16 global monolayer samples and NNE samples to making it the most toxic of the six PFAS. Further validation of gene expression levels showed that the TGF-β signaling pathways were involved in the early global developmental toxicity and in the early skin developmental toxicity of PFOS. Interestingly, our results showed that PFOS inhibited the ciliogenesis of NNE cells, which may interfere with the transduction of TGF-β, Notch, Hedgehog, and Hippo signaling pathways, ultimately inhibiting early embryonic skin development and posing a potential threat to the occurrence of congenital skin diseases. Overall, our study suggests a potential toxicity mechanism by which PFAS inhibit ciliogenesis to interfere with the transduction of important signaling pathways, leading to early global developmental toxicity as well as early embryonic skin developmental toxicity and potential congenital skin diseases.
Published in
Understanding the effects of per- and polyfluoroalkyl substances on early skin development: Role of ciliogenesis inhibition and altered microtubule dynamics
Zhao M, Yin N, Yang R et al. · The Science of the total environment 2024 · PMID 38163615 · doi:10.1016/j.scitotenv.2023.169702
This dataset
Open GSE236956 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 GSE236956_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 PRJNA993187 and SRA study SRP448372. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38163615) ↗
Study design
42 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 42 sample titles: 42 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

+ 2 more — browse all 42 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.