GEO series

Integrated small and long RNA sequencing in single oocytes reveals piRNA-mediated transposon repression during human oogenesis

GSE296363 Homo sapiens (human) Non-coding RNA profiling 46 samples Submitted 2026/02/06 Platform GPL20795

At a glance

Non-coding RNA profiling · human · 46 samples

What it is: Non-coding RNA profilingLevels of RNAs that do not code for proteins, such as miRNA or lncRNA.
Organism: Homo sapiens (human)
Samples: 46 samples
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: Integrated small and long RNA sequencing reveals piRNA mediated transposon repression during human oogenesisNature communications · 2026

Summary (written by the submitters)

In this study, we simultaneously profiled small and long RNA transcriptomes in individual human oocytes across four developmental stages. piRNAs, especially PIWIL3-associated short piRNAs (short-piRNAs), are the predominant small non-coding RNAs during human oogenesis. A marked increase in short-piRNAs after the primordial follicle stage coincided with a global downregulation of TE expression, particularly LINE-1 (L1) and endogenous retroviruses (ERVs).

Read the full summary ↓

On the other hand, PIWIL1- and PIWIL2-associated long piRNAs (long-piRNAs) were correlated with the silencing of certain specific ERV subfamilies. Genomic-context analyses revealed that highly productive piRNA clusters have evolved asymmetric antisense insertion bias toward L1 and ERVs, contributing to TE families-specific regulation.

Published in

Integrated small and long RNA sequencing reveals piRNA mediated transposon repression during human oogenesis

Zhang F, Zhang H, Xiao Y et al. · Nature communications 2026 · PMID 41813703 · doi:10.1038/s41467-026-70296-4

This dataset

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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 GSE296363_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 ↗

Also filed as BioProject PRJNA1258992 and SRA study SRP583128. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41813703) ↗

Samples in this study

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+ 46 more — browse all 46 samples with per-sample file links →

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