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Series GSE121922 Query DataSets for GSE121922
Status Public on Jun 13, 2019
Title Transcriptomic and gene ontology profiling of the human corneal cell types
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: To identify distinct gene expression and functional profiles for the three main cell types (epithelial, keratocyte and endothelial) of the human cornea. Methods: RNA-sequencing was performed using total RNA isolated from ex vivo corneal epithelial cells (evCEpC), keratocytes (evK) and endothelial cells (evCEnC) obtained from 3 donor corneas obtained from a commercial eye bank. Transcriptomic analysis was performed using Kallisto (alignment (hg38) and quantification) and Sleuth (differential gene expression(DGE)), with transcript abundances calculated as transcripts per kilobase million (TPM). Expression was defined as TPM≥7.5 and significant DGE as a fold-change ≥4 and a false-discovery rate adjusted p-value≤0.05. Cell type specificity was defined as genes adhering to the above expression and DGE criteria and not expressed (i.e., TPM<7.5) in the other two cell types. Gene ontology enrichment analysis was performed on the cell type-specific gene lists using the gene group functional profiling (g:GOSt) tool within the web-based g:Profiler suite. Results: We identified 205 genes specific in evCEpC, and enrichment of epithelial-associated GO terms (e.g., cornified envelope, epidermis development, cell-cell adhesion). We identified 76 genes specific in evK, and fibroblast-associated GO terms (e.g., collagen metabolic process, metallopeptidase activity, extracellular matrix organization). We identified 96 genes specific in evCEnC, and at least one CEnC-associated GO term (e.g., cellular cation homeostasis) but several synapse-associated GO terms (e.g., synapse organization, synapse part). Conclusions: The human cornea is comprised of three main cell types that play important roles in maintaining corneal clarity and vision. Our results demonstrate that a small subset (0.4-1%) of the protein-coding genes confers distinct and classic functional properties associated with each cell type. In addition, we identified a novel association and significant functional overlap between CEnC and synapses. This may lead to insights into the molecular mechanisms of transendothelial transport and secretion, which are integral metabolic features of the corneal endothelium.
 
Overall design Corneal epithelium, corneal endothelium and corneal stroma were isolated from three donor corneas (i.e., 3 biological replicates). Keratocyte RNA was isolated from corneal stroma tissue.
 
Contributor(s) Frausto RF, Swamy VS, Aldave AJ
Citation(s) 31194824, 26337789, 32366916
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 EY022082 Identification and Characterization of the Genetic Basis of PPCD UNIVERSITY OF CALIFORNIA LOS ANGELES ANTHONY John ALDAVE
Submission date Oct 29, 2018
Last update date May 12, 2020
Contact name Anthony J. Aldave
E-mail(s) Aldave@jsei.ucla.edu
Organization name Stein Eye Institute, UCLA
Department Ophthalmology
Lab Cornea Genetics Laboratory
Street address 200 Stein Plaza DSERC 3-143
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (9)
GSM3449987 evCEpC_1
GSM3449988 evCEpC_2
GSM3449989 evCEpC_3
Relations
BioProject PRJNA499078
SRA SRP167143

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Supplementary file Size Download File type/resource
GSE121922_All_Processed_Data.txt.gz 834.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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