Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Small RNA-seq Aqueous humor of human glaucoma (open-angle glaucoma and pseudoexfoliative glaucoma) patients against cataract

ABSTRACT: Study investigates the biological role of small RNAs present in aqueous humor in patients with primary open-angle glaucoma, pseudoexfoliative glaucoma, and cataract, with the aim of identifying molecular biomarkers and improving understanding of disease mechanisms. Aqueous humor samples were collected during ophthalmic surgery, followed by RNA extraction from the cell-free supernatant using a commercial kit designed for low-input RNA. Small RNA sequencing libraries were prepared using adapter ligation with Unique Molecular Identifiers, reverse transcription, PCR amplification, and magnetic bead purification, and library quality was assessed using a microfluidics-based system. The pooled libraries were sequenced using paired-end sequencing on an Illumina NextSeq platform, and the resulting FASTQ files were used for downstream bioinformatic and machine learning analyses integrating molecular, clinical, and imaging data.

INSTRUMENT(S): NextSeq 2000

ORGANISM(S): Homo sapiens

SUBMITTER: Piotr Karabowicz

PROVIDER: E-MTAB-16859 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Similar Datasets

Project description:Glaucoma is a neurodegenerative disease in which vision is lost as a result of the apoptosis of retinal ganglion cells. When the trabecular meshwork cells, that regulate aqueous humor outflow, are stressed as they are in some forms of glaucoma, they considerably up-regulated secretion of a protein called myocilin into the aqueous. The function of this protein is unclear; but since some aqueous humor flows to the posterior of the eye, the effects of myocilin will also be felt by the retinal cells. We have a transgenic mouse that secretes large amounts of myocilin into aqueous humor. In these mice, there is a deposition of myocilin on membranes of certain cells suggesting myocilin might have some signaling functions. This signaling function could explain why stresses that increase intraocular pressures can increase the likelihood for glaucoma, cause the myocilin to be secreted at very high levels by the trabecular meshwork. Myocilin may be important in treating glaucoma. This experiment will determine if myocilin is altering gene expression in the retina. The results should show variations in expression levels and will give us some indication of the pathways that are important to preserve retinal ganglion cells after a diagnosis of glaucoma. Our hypothesis is that myocilin is acting like a signaling protein in the eye. It acts not only in the anterior segment but also in retina as a result of the flow of some aqueous to the back of the eye. This signaling function is protective to certain ocular cells. This function of myocilin may influence cells in the retina and may counter the apoptotic signals in the retinal ganglion cells that occur during glaucoma. Retinas from transgenic mice and from mice of the same strain that do not have the transgene will be dissected. The mice will be three weeks of age. Because of the small size of the retina, samples will be pooled to obtain the RNA necessary to run the microarray. Three control and three transgenic samples will be run and compared with each other. We have data indicating that myocilin is at high levels in the aqueous humor of the transgenic animals.

Dataset Information

Small RNA-seq Aqueous humor of human glaucoma (open-angle glaucoma and pseudoexfoliative glaucoma) patients against cataract

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets