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SRX4950955: GSM3449993: evCEnC_1; Homo sapiens; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2500) run: 13.4M spots, 669.5M bases, 270.6Mb downloads

Submitted by: NCBI (GEO)
Study: Transcriptomic and gene ontology profiling of the human corneal cell types
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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.
Sample: evCEnC_1
SAMN10341958 • SRS3993141 • All experiments • All runs
Organism: Homo sapiens
Instrument: Illumina HiSeq 2500
Strategy: RNA-Seq
Selection: cDNA
Layout: SINGLE
Construction protocol: TriReagent extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNeasy Clean-Up Kit. Enrichment for poly(A) RNAs was performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module, followed by library preparation using the PrepX Complete ILM DNA Library Kit. Libraries were prepared as per the manufacturer's instructions.
Experiment attributes:
GEO Accession: GSM3449993
Runs: 1 run, 13.4M spots, 669.5M bases, 270.6Mb
Run# of Spots# of BasesSizePublished


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