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Series GSE242990 Query DataSets for GSE242990
Status Public on Sep 22, 2023
Title Multi-omics analysis identifies coordination and hierarchy of transcription factors controlling specific epithelial cell fates in corneal epithelium [Bulk RNA-seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary The homeostasis of the transparent corneal epithelium in the eye is maintained by the proliferation and differentiation of limbal stem cells that possess the proper cell fate. A potential disease mechanism underlying corneal opacity has been proposed to be limbal stem cells acquiring the cell fate of keratinocytes in the non-transparent epidermis. In this study, we performed a multi-omics analysis of human limbal stem cells derived from the cornea and keratinocytes from the epidermal stratum basale and characterized the similar yet distinct molecular signatures of these cells. By gene regulatory network analysis, we identified cell fate defining transcription factors and their regulatory hierarchy that are shared by the two cell types and those that regulate specific epithelial programs. Our findings indicate that shared transcription factors often regulate limbal stem cell-specific transcription factors. Single-cell RNA-seq analysis of the cornea and the epidermis confirms the shared and specific transcription factor expression patterns in the stem cells of these tissues. Finally, we showed that genes associated with corneal opacity can cooperatively be targeted by the shared and limbal stem cell-specific transcription factors. By characterizing molecular signatures, our study uncovers the distinct regulatory circuitry controlling limbal stem cell fates and corneal opacity.
 
Overall design siRNA knockdown of PAX6 and FOSL2 in various Limbal stem cells
 
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 Sep 12, 2023
Last update date Oct 26, 2023
Contact name Jo Huiqing Zhou
E-mail(s) jo.zhou@radboudumc.nl
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 (14)
GSM7776583 PAX6KD_1
GSM7776584 PAX6CTRL_1
GSM7776585 PAX6KD_2
This SubSeries is part of SuperSeries:
GSE206924 Multi-omics analyses identify transcription factor interplay in corneal epithelial fate determination and disease
Relations
BioProject PRJNA1015691

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE242990_bulkRNAseq_table_knockdown.tsv.gz 612.4 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA

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