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Series GSE236904 Query DataSets for GSE236904
Status Public on Dec 27, 2023
Title Integrated single-cell multiomics uncovers foundational regulatory mechanisms of lens development and pathology [CUT&RUN]
Organism Gallus gallus
Experiment type Other
Summary Ocular lens development entails epithelial to fiber cell differentiation, defects in which cause congenital cataract. We report the first single-cell multiomic atlas of lens development, leveraging snRNA-seq, snATAC-seq, and CUT&RUN-seq to discover novel mechanisms of cell fate determination and cataract-linked regulatory networks. A comprehensive profile of cis- and trans-regulatory interactions, including for the cataract-linked transcription factor MAF, is established across a temporal trajectory of fiber cell differentiation. Further, we divulge a conserved epigenetic paradigm of cellular differentiation, defined by progressive loss of H3K27 methylation writer Polycomb repressive complex 2 (PRC2). PRC2 localizes to heterochromatin domains across master-regulator transcription factor gene bodies, suggesting it safeguards epithelial cell fate. Moreover, we demonstrate that FGF hyper-stimulation in vivo leads to MAF network activation and the emergence of novel lens cell states. Collectively, these data depict a comprehensive portrait of lens fiber cell differentiation, while defining regulatory effectors of cell identity and cataract formation. 
 
Overall design Cleavage Under Targets and Release Using Nuclease sequencing (CUT&RUN-seq) was performed according to manufacturer protocol, with slight modification, as described. Chicken embryos were obtained from Michigan State University and lenses were dissected from embryonic day 4.5 chicken embryos. Dissected lenses were collected on ice and pooled into 3 biological replicates consisting of approximately 44 lenses each. Histone modifications and PRC2 complex members were assayed, as described.
Web link https://doi.org/10.1242/dev.202249
 
Contributor(s) Tangeman JA, Rebull SM, Grajales-Esquivel E, Weaver JM, Bendezu-Sayas S, Robinson ML, Lachke SA, Del Rio-Tsonis K
Citation(s) 38180241
Submission date Jul 10, 2023
Last update date Mar 28, 2024
Contact name Katia Del Rio-Tsonis
E-mail(s) delriok@miamioh.edu
Organization name Miami University
Department Biology
Street address 700 E High St
City Oxford
State/province OH
ZIP/Postal code 45056
Country USA
 
Platforms (1)
GPL24517 HiSeq X Ten (Gallus gallus)
Samples (20)
GSM7585108 IgG_1
GSM7585109 IgG_2
GSM7585110 H3K4me3_1
This SubSeries is part of SuperSeries:
GSE236905 Integrated single-cell multiomics uncovers foundational regulatory mechanisms of lens development and pathology.
Relations
BioProject PRJNA993026

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
GSE236904_AEBP2_peaks.narrowPeak.gz 3.0 Mb (ftp)(http) NARROWPEAK
GSE236904_EZH2_peaks.narrowPeak.gz 646.0 Kb (ftp)(http) NARROWPEAK
GSE236904_H3K27me3_peaks.narrowPeak.gz 569.9 Kb (ftp)(http) NARROWPEAK
GSE236904_H3K4me3_peaks.narrowPeak.gz 309.2 Kb (ftp)(http) NARROWPEAK
GSE236904_JARID2_peaks.narrowPeak.gz 1.0 Mb (ftp)(http) NARROWPEAK
GSE236904_SUZ12_peaks.narrowPeak.gz 1.2 Mb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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