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Series GSE206918 Query DataSets for GSE206918
Status Public on Sep 22, 2023
Title Multi-omics analyses identify transcription factor interplay in corneal epithelial fate determination and disease [ATAC-seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The transparent corneal epithelium in the eye is maintained through the homeostasis regulated by limbal stem cells, while the non-transparent epidermis relies on epidermal keratinocytes for renewal. Despite their cellular similarities, the precise cell fates of these two types of epithelial stem cells, which give rise to functionally distinct epithelia, remain unknown. We performed a multi-omics analysis of human limbal stem cells from the cornea and keratinocytes from the epidermis and characterized their molecular signatures, highlighting their similarities and differences. Through gene regulatory network analyses, we identified shared and cell type-specific transcription factors that define specific cell fates, and established their regulatory hierarchy. Single-cell RNA-seq analyses of the cornea and the epidermis confirmed these shared and cell type-specific transcription factors. Notably, the shared and limbal stem cell-specific transcription factors can cooperatively target genes associated with corneal opacity. Importantly, we discovered that FOSL2, a direct PAX6 target gene, is a novel candidate associated with corneal opacity, and it regulates genes implicated in corneal diseases. By characterizing molecular signatures, our study unveils the regulatory circuitry governing the limbal stem cell fate and its association with corneal opacity.

Overall design Comparative genome accesibilty analysis of ATAC-seq data for Limbal Stem Cells and Keratinocytes
Contributor(s) Smits JG, Cunha DL, Amini M, Bertolin M, Laberthonnière C, Qu J, Owen N, Latta L, Seitz B, Roux LN, Stachon T, Ferrari S, Moosajee M, Aberdam D, Szentmary N, van Heeringen SJ, Zhou H
Citation(s) 37856539
Submission date Jun 24, 2022
Last update date Oct 26, 2023
Contact name Jo Huiqing Zhou
Organization name Radboud University
Street address Geert Grooteplein 26/18
City Nijmegen
ZIP/Postal code 6525GA
Country Netherlands
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (10)
GSM6266861 KC_ATAC_1
GSM6266862 KC_ATAC_2
GSM6266863 KC_ATAC_3
This SubSeries is part of SuperSeries:
GSE206924 Multi-omics analyses identify transcription factor interplay in corneal epithelial fate determination and disease
BioProject PRJNA852601

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SOFT formatted family file(s) SOFTHelp
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Supplementary file Size Download File type/resource
GSE206918_RAW.tar 686.7 Mb (http)(custom) TAR (of BW, NARROWPEAK)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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