Gene Expression
Nebulas
Gene Expression NebulasSummary: To understand better the factors contributing to keratoconus (KTCN), we used RNA sequencing to perform a transcriptome profile of human KTCN corneas. Over 82% of the genes and almost 75% of the transcripts detected as differentially expressed in KTCN and non-KTCN corneas were confirmed in the replication study using another set of samples. We used these differentially expressed genes to generate a network of KTCN-deregulated genes. We found an extensive disruption of collagen synthesis and maturation pathways, as well as downregulation of the core elements of the TGF-β, Hippo, and Wnt signaling pathways influencing corneal organization. We identified long noncoding RNAs (lncRNAs) and conducted a computational analysis of their potential functions, and found that lncRNAs regulated the processing and expression of the aforementioned genes. This first comprehensive transcriptome profiling of human KTCN corneas points further to a complex etiology of KTCN.
Overall Design: Transcription profiling of 25 KTCN and 25 non-KTCN corneas using RNA-Seq
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| Growth Protocol: | - |
| Treatment Protocol: | - |
| Extract Protocol: | Total RNA extraction and purification steps were performed according to the manufacturer’s instructions supplied with a Total RNA Purification Kit (Norgen Biotek). |
| Library Construction Protocol: | Libraries were prepared with a TruSeq Stranded Total RNA LT with Ribo-Zero™ Human/Mouse/Rat Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol, with slight modifications. |
| Molecule Type: | rRNA- RNA |
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| Library Layout: | PAIRED |
| Library Strand: | Forward |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina HiSeq 1500 |
| Strand-Specific: | Specific |