GEO series

Lactate and histone H3K18 lactylation are associated with metabolic control of gene expression in the retina [explant_RNA-seq]

GSE291661 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2026/03/02 Platform GPL30172

At a glance

RNA-seq (gene expression) · mouse · 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: Mus musculus (mouse)
Samples: 12 samples: 6 conditions, mostly in duplicateGroups 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: Lactate and histone H3K18 lactylation are associated with metabolic control of gene expression in the retinaPLoS genetics · 2026

Summary (written by the submitters)

High aerobic glycolysis in retinal photoreceptors, as in cancer cells, is implicated in mitigating energy and metabolic demands. Lactate, a key product of glycolysis, is implicated in epigenetic regulation through histone lactylation in cancer. Here, we demonstrate that increased ATP production during retinal development is achieved primarily through augmented glycolysis.

Read the full summary ↓

Histone lactylation, especially H3K18La, parallels enhanced glycolysis and its product, lactate, in developing retina and in retinal explants. Multi-omics analyses, combined with confocal imaging, reveal the localization of H3K18La near H3K27Ac in euchromatin at promoters of active retinal, especially photoreceptor, genes. H3K18La and gene expression also correspond to glucose metabolism in retinal explants. Evaluation of accessible chromatin at H3K18La promoters uncovers an enrichment of GC-rich motifs for transcription factors of SP, KMT and KLF families, among others, indicating specificity of H3K18La-mediated gene regulation. Our results highlight glycolysis/lactate/H3K18La as a regulatory axis in fine-tuning gene expression in developing and mature retina.

Published in

Lactate and histone H3K18 lactylation are associated with metabolic control of gene expression in the retina

Gaur M, Brooks MJ, Liang X et al. · PLoS genetics 2026 · PMID 41950290 · doi:10.1371/journal.pgen.1012100

This dataset

Open GSE291661 in finder → Find more mouse 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 GSE291661_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 PRJNA1234617 and SRA study SRP569640. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41950290) ↗

Study design

6 conditions, mostly in duplicate

5mM glucose, RNA-seq, biological replicate 1,… ×2 5mM glucose, RNA-seq, biological replicate 2,… ×2 5mM glucose, RNA-seq, biological replicate 3,… ×2 25mM glucose, RNA-seq, biological replicate 1… ×2 25mM glucose, RNA-seq, biological replicate 2… ×2 25mM glucose, RNA-seq, biological replicate 3… ×2

Supports a between-group comparison across 12 samples.

How we read this: 6 replicated groups read from 12 sample titles; they account for 12 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

GSM8839498 5mM glucose, RNA-seq, biological replicate 1, technical replicate 1 5mM glucose, RNA-seq, b…
GSM8839499 5mM glucose, RNA-seq, biological replicate 1, technical replicate 2 5mM glucose, RNA-seq, b…
GSM8839500 5mM glucose, RNA-seq, biological replicate 2, technical replicate 1 5mM glucose, RNA-seq, b…
GSM8839501 5mM glucose, RNA-seq, biological replicate 2, technical replicate 2 5mM glucose, RNA-seq, b…
GSM8839502 5mM glucose, RNA-seq, biological replicate 3, technical replicate 1 5mM glucose, RNA-seq, b…
GSM8839503 5mM glucose, RNA-seq, biological replicate 3, technical replicate 2 5mM glucose, RNA-seq, b…
GSM8839504 25mM glucose, RNA-seq, biological replicate 1, technical replicate 1 25mM glucose, RNA-seq, …
GSM8839505 25mM glucose, RNA-seq, biological replicate 1, technical replicate 2 25mM glucose, RNA-seq, …
GSM8839506 25mM glucose, RNA-seq, biological replicate 2, technical replicate 1 25mM glucose, RNA-seq, …
GSM8839507 25mM glucose, RNA-seq, biological replicate 2, technical replicate 2 25mM glucose, RNA-seq, …
GSM8839508 25mM glucose, RNA-seq, biological replicate 3, technical replicate 1 25mM glucose, RNA-seq, …
GSM8839509 25mM glucose, RNA-seq, biological replicate 3, technical replicate 2 25mM glucose, RNA-seq, …

Datasets on a similar topic

GSE291663 Lactate and histone H3K18 lactylation are associated with metabolic control of gene expression in the retina [explant_CUT&Tag] 10 samples shares h3k18, lactylation, lactate, histone, control, explant, retina
GSE291677 Lactate and histone H3K18 lactylation are associated with metabolic control of gene expression in the retina 38 samples shares h3k18, lactylation, lactate, histone, control, retina
GSE251640 Dux promotes metabolism-lactylation-MET cascaded network during early iPSC reprogramming with Brg1 as the histone lactylation reader [RNA-Seq] 12 samples shares lactylation, histone, rna-seq
GSE318448 Pharmacological elevation of lactate alleviates sepsis via histone lactylation-induced IL-10 production 10 samples shares lactylation, lactate, histone
GSE290816 Cell autonomous regional differences in oligodendrocyte precursor cell development and response to oncohistone H3.3 K27M [RNA-seq] 142 samples shares histone, rna-seq
GSE263060 Addressing the specific roles of histone modifications in transcriptional repression [RNA-seq] 105 samples shares histone, rna-seq
GSE294512 eIF4G2-mediated Translation Initiation of Histone Modifiers is Essential for Intestinal Stem Cell Maintenance and Differentiation [RNA-seq] 92 samples shares histone, rna-seq
GSE285141 Histone H3.3 ensures cell proliferation and genomic stability during myeloid cell development [RNA-seq] 81 samples shares histone, rna-seq

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