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KROX20-Notch1 Network Transcriptionally Regulates Meibomian Gland Stem Cells for Its Development and Homeostasis [ChIP-Seq]

GSE289069 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 11 samples Submitted 2025/11/01 Platform GPL21697
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 11 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Homo sapiens (human)
Samples
11 samples: 3 × IHMGECs, infected by pLenti-Krox20, post 42 hour infection, pulldown by anti-Krox20, biol vs 3 × IHMGECs, pulldown by anti-Histone H3, biol vs 3 × IHMGECs, input, biol vs 2 × IHMGECs, infected by pLenti-GFP, post 42 hour infection, pulldown by anti-Krox20, biolGroups 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
Disruption of Krox20-Notch1 signaling blocks meibomian gland development and homeostasis leading to dry eye diseaseNature communications · 2025
Summary (written by the submitters)
Meibomian gland dysfunction is the leading cause of Evaporative Dry Eye Disease (EDED), and accounts for approximately 90% of dry eye disease cases worldwide. The transcription factor Krox20 has been shown to mark stem cells that play a critical role in Meibomian gland (MG) development and homeostasis, however, the molecular mechanisms underlying these processes are not well understood.
Read the full summary ↓
In this report, we used multiple Krox20 lineage tracing and ablation studies to investigate the process that governs lineage commitment during MG morphogenesis and homeostasis. Krox20 marks MG stem/progenitor cell pools, and it regulates cellular contributions to the glands, as loss of Krox20 leads to MG atrophy, while its overexpression results in MG enlargement. We also found that Notch1 signaling is regulated by KROX20 and that ablation of the Notch1 gene in KROX20-expressing cells leads to MG atrophy, while Notch1 overexpression partially rescues MG atrophy caused by the loss of Krox20. Together, these results reveal a critical KROX20-Notch1 regulatory pathway in MG stem/progenitor cells. Activation of Notch1 signaling may offer a novel approach to preventing and treating EDED caused by the depletion of the MG stem cell pool that can occur with aging.
Published in
Disruption of Krox20-Notch1 signaling blocks meibomian gland development and homeostasis leading to dry eye disease
Zhang Y, Tchegnon E, Ghotbi E et al. · Nature communications 2025 · PMID 41276517 · doi:10.1038/s41467-025-66740-6
This dataset
Open GSE289069 in finder → Find more human ChIP / ATAC / CUT&Tag 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 GSE289069_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1220984 and SRA study SRP562280. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41276517) ↗
Study design
3 × IHMGECs, infected by pLenti-Krox20, post 42 hour infection, pulldown by anti-Krox20, biol vs 3 × IHMGECs, pulldown by anti-Histone H3, biol vs 3 × IHMGECs, input, biol vs 2 × IHMGECs, infected by pLenti-GFP, post 42 hour infection, pulldown by anti-Krox20, biol

Supports a between-group comparison across 11 samples.

How we read this: 4 replicated groups read from 11 sample titles; they account for 11 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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