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LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs

GSE232939 Homo sapiens (human) RNA-seq (gene expression) 112 samples Submitted 2024/09/07 Platform GPL30173Platform GPL16791Platform GPL34281Platform GPL18573Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 112 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
112 samples: 95 distinct titles, 17 of them repeatedGroups 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
LINE1 and PRC2 control nucleolar organization and repression of the 8C state in human ESCsDevelopmental cell · 2025
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
LINE1 and PRC2 control nucleolar organization and repression of the 8C state in human ESCs
Zhang J, Ataei L, Mittal K et al. · Developmental cell 2025 · PMID 39413784 · doi:10.1016/j.devcel.2024.09.024
This dataset
Open GSE232939 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 GSE232939_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 PRJNA974446 and SRA study SRP499943. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39413784) ↗
Study design
95 distinct titles, 17 of them repeated
Rep1, ASO-L ×2 Rep2, ASO-L ×2 Rep1, +UNC ×2 Rep2, +UNC ×2 Rep3, +UNC ×2 Naive_HESC_RSeT_DT ×2 Naive_HESC_R ×2 Primed_HESC ×2 +9 more

How we read this: Read from 112 sample titles: 95 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

+ 72 more — browse all 112 samples with per-sample file links →

Datasets on a similar topic

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.