GEO series

Single-cell analysis of follicular fluid reveals dysregulation of ovulatory immune function in Polycystic Ovary Syndrome patients undergoing ovarian stimulation

GSE313660 Homo sapiens (human) Single-cell RNA-seq 16 samples Submitted 2026/07/07 Platform GPL34281

At a glance

Single-cell RNA-seq · human · 16 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Homo sapiens (human)
Samples: 16 samples: 2 × Obese control feature barcode vs 2 × Obese control gene expression vs 2 × Obese PCOS feature barcode vs 2 × Obese PCOS gene expressionGroups 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: Single-cell analysis of follicular fluid reveals dysregulation of ovulatory immune function in Polycystic Ovary Syndrome patients undergoing ovarian stimulation†Biology of reproduction · 2026

Summary (written by the submitters)

Polycystic ovary syndrome is the most common endocrine condition in women and anovulatory cause of female infertility. While a pro-inflammatory cytokines and leukocyte bias in systemic circulation is well-documented in PCOS, it is not known how this inflammation extends to or affects the ovary. Additionally, the relationship between ovulation and inflammation in PCOS is not well-defined.

Read the full summary ↓

We hypothesize that the ovarian follicular immune environment in PCOS is uniquely dysregulated, and that resolving anovulation through ovulation induction is not sufficient to alleviate this dysregulation. Using single-cell RNA and surface protein analysis of peripheral blood and follicular fluid from patients undergoing in vitro fertilization, we discovered that both control and PCOS follicles were immunologically distinct from circulation. At a systemic level, we find that ovulation induction in PCOS does not alleviate systemic inflammation. In contrast, while healthy control ovaries experienced acute immune-directed ovulatory signaling, PCOS ovarian follicles were deficient in key pro-ovulatory cell to cell communication, and displayed instead a chronic low-grade inflammatory state with fibrotic features. Taken together, a picture emerges where acute ovulation demonstrates a well-ordered series of follicle-specific immune information flows, which are disrupted and replaced by low grade chronic inflammation in the PCOS follicle.

Published in

Single-cell analysis of follicular fluid reveals dysregulation of ovulatory immune function in Polycystic Ovary Syndrome patients undergoing ovarian stimulation†

Wegrzynowicz AK, Banerjee S, Grimes E et al. · Biology of reproduction 2026 · PMID 41766605 · doi:10.1093/biolre/ioag051

This dataset

Open GSE313660 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 GSE313660_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1299291 and SRA study SRP605486. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41766605) ↗

Study design

2 × Obese control feature barcode vs 2 × Obese control gene expression vs 2 × Obese PCOS feature barcode vs 2 × Obese PCOS gene expression

Supports a between-group comparison across 8 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 8 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

GSM9371983 Obese control feature barcode 1 Obese control feature b…
GSM9371984 Obese control gene expression 1 Obese control gene expr…
GSM9371985 Normal weight PCOS feature barcode
GSM9371986 Normal weight PCOS gene expression
GSM9371987 Obese PCOS feature barcode 1 Obese PCOS feature barc…
GSM9371988 Obese PCOS gene expression 1 Obese PCOS gene express…
GSM9371989 Overweight PCOS feature barcode
GSM9371990 Overweight PCOS gene expression
GSM9371991 Obese control feature barcode 2 Obese control feature b…
GSM9371992 Obese control gene expression 2 Obese control gene expr…
GSM9371993 Overweight control feature barcode
GSM9371994 Overweight control gene expression
GSM9371995 Obese PCOS feature barcode 2 Obese PCOS feature barc…
GSM9371996 Obese PCOS gene expression 2 Obese PCOS gene express…
GSM9371997 Normal weight control feature barcode
GSM9371998 Normal weight control gene expression

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