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Loss of H3K9me3 maintenance leads in human neural progenitor cells leads to transcriptional activation of L1 retrotransposons [Bulk RNA-seq]

GSE292899 Homo sapiens (human) RNA-seq (gene expression) 20 samples Submitted 2026/02/11 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 20 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
20 samples: 7 conditions, mostly in triplicateGroups 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
Loss of SETDB1-mediated H3K9me3 in human neural progenitor cells leads to transcriptional activation of L1 retrotransposonsNucleic acids research · 2026
Summary (written by the submitters)
We used CRISPRi-mediated deletion of the H3K9me3 methyltransferase SETDB1 in a human neural epithelial-like stem cell line with the characteristics of human neural progenitor cells (hNPCs) to model disruption of heterochromatin maintenance. We found that a key event following the loss of H3K9me3 maintenance was the expression of evolutionary young full-length L1 elements. Transcriptional activation of L1s was associated with a loss of CpG DNA methylation at their promoters, suggesting that deposition of H3K9me3 at the L1 promoter is required to maintain DNA methylation.
Published in
Loss of SETDB1-mediated H3K9me3 in human neural progenitor cells leads to transcriptional activation of L1 retrotransposons
Karlsson O, Pandiloski N, Horvath V et al. · Nucleic acids research 2026 · PMID 41641702 · doi:10.1093/nar/gkag100
This dataset
Open GSE292899 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 GSE292899_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 PRJNA1241830 and SRA study SRP573015. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41641702) ↗
Study design
7 conditions, mostly in triplicate
SETDB1_CRISPRi_Control ×4 MORC2_CRISPRi ×3 MORC2_TRIM28_double_CRISPRi_MOI4 ×3 TRIM28_CRISPRi ×3 TRIM28_MORC2_CRISPRi_Control ×3 SETDB1_CRISPRi_guide2 ×2 SETDB1_CRISPRi_guide1 ×2

Supports a between-group comparison across 20 samples.

How we read this: 7 replicated groups read from 20 sample titles; they account for 20 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
Datasets on a similar topic

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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.