GEO series

An environmentally relevant mixture of Perfluoroalkyl Substances (PFAS) impacts proliferation, steroid hormone synthesis, and gene transcription in primary human granulosa cells

GSE246371 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2024/07/03 Platform GPL20301

At a glance

RNA-seq (gene expression) · human · 12 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: 12 samples: 12 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: An environmentally relevant mixture of per- and polyfluoroalkyl substances (PFAS) impacts proliferation, steroid hormone synthesis, and gene transcription in primary human granulosa cellsToxicological sciences : an official journal of the Society of Toxicology · 2024

Summary (written by the submitters)

Perfluoroalkyl substances (PFAS) are a group of synthetic chemicals that are resistant to biodegradation and are environmentally persistent. PFAS are found in many consumer products including non-stick cookware, food packaging materials, upholstery, and personal care products. Accordingly, PFAS are a major source of water and soil contamination.

Read the full summary ↓

Although use of many PFAS have been phased out, they continue to be detected in human and animal fluids, including human follicular fluid. This study investigated the effects of an environmentally relevant PFAS mixture [perfluorooctanoic acid (PFOA), perfluorooctanesulfonic acid (PFOS), perfluorohexanesulfonic acid (PFHxS)] on the transcriptome and function of human granulosa cells (hGCs). PFOA, PFOS, and PFHxS were detected in 100% of follicle fluid samples. Increased cell proliferation was observed in hGCs treated with the PFAS mixture with no impacts on cellular apoptosis. The PFAS mixture also altered steroid hormone synthesis, increasing both FSH-stimulated and basal progesterone secretion and concomitant upregulation of STAR protein. RNA sequencing revealed inherent differences in transcriptomic profiles in hGCs after PFAS exposure. This study demonstrates functional and transcriptomic changes in hGCs after exposure to a PFAS mixture, improving our knowledge about the impacts of PFAS exposures and female reproductive health. These findings suggest that PFAS compounds have the potential to disrupt normal granulosa cell function with possible long-term consequences on overall reproductive health.

Published in

An environmentally relevant mixture of per- and polyfluoroalkyl substances (PFAS) impacts proliferation, steroid hormone synthesis, and gene transcription in primary human granulosa cells

Clark KL, Shukla M, George JW et al. · Toxicological sciences : an official journal of the Society of Toxicology 2024 · PMID 38603627 · doi:10.1093/toxsci/kfae049

This dataset

Open GSE246371 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 GSE246371_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 PRJNA1032615 and SRA study SRP468643. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38603627) ↗

Study design

12 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 12 sample titles: 12 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

GSM7867771 Granulosa cells, 84_Pre-Treatment
GSM7867772 Granulosa cells, 84_Post-Treatment
GSM7867773 Granulosa cells, 89_Pre-Treatment
GSM7867774 Granulosa cells, 89_Post-Treatment
GSM7867775 Granulosa cells, 92_Pre-Treatment
GSM7867776 Granulosa cells, 92_Post-Treatment
GSM7867777 Granulosa cells, 113_Pre-Treatment
GSM7867778 Granulosa cells, 113_Post-Treatment
GSM7867779 Granulosa cells, 114_Pre-Treatment
GSM7867780 Granulosa cells, 114_Post-Treatment
GSM7867781 Granulosa cells, 123_Pre-Treatment
GSM7867782 Granulosa cells, 123_Post-Treatment

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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.