DOI: 10.5061/dryad.s1rn8pkhb
title: Transcriptional responses in a mouse model of silicone wire embolization induced acute retinal artery Ischemia and Reperfusion

description: Acute retinal ischemia and ischemia-reperfusion injury are the primary
 causes of retinal neural cell death and vision loss in retinal artery
 occlusion (RAO). The absence of an accurate mouse model for simulating the
 retinal ischemic process has hindered progress in developing
 neuroprotective agents for RAO. We developed a unilateral pterygopalatine
 ophthalmic artery occlusion (UPOAO) mouse model using silicone wire
 embolization combined with carotid artery ligation. The survival of
 retinal ganglion cells and visual function were evaluated to determine the
 duration of ischemia. Immunofluorescence staining, optical coherence
 tomography, and haematoxylin and eosin staining were utilized to assess
 changes in major neural cell classes and retinal structure degeneration at
 two reperfusion durations. Transcriptomics was employed to investigate
 alterations in the pathological process of UPOAO following ischemia and
 reperfusion, highlighting transcriptomic differences between UPOAO and
 other retinal ischemia-reperfusion models. The UPOAO model successfully
 replicated the acute interruption of retinal blood supply observed in RAO.
 60-minutes of ischemia led to significant loss of major retinal neural
 cells and visual function impairment. Notable thinning of the inner
 retinal layer, especially the ganglion cell layer, was evident post-UPOAO.
 Temporal transcriptome analysis revealed various pathophysiological
 processes related to immune cell migration, oxidative stress, and immune
 inflammation during the non-reperfusion and reperfusion periods. A
 pronounced increase in microglia within the retina and peripheral
 leukocytes accessing the retina was observed during reperfusion periods.
 Comparison of differentially expressed genes (DEGs) between the UPOAO and
 high intraocular pressure models revealed specific enrichments in lipid
 and steroid metabolism-related genes in the UPOAO model. The UPOAO model
 emerges as a novel tool for screening pathogenic genes and promoting
 further therapeutic research in RAO.
description: Retinal samples from UPOAO, HIOP, and UCCAO mice were extracted
 and promptly frozen in liquid nitrogen within 10 minutes of cervical
 dislocation. Total RNA extraction was performed according to the protocol
 outlined in the TRIzol Reagent manual (Life Technologies, CA, USA). RNA
 integrity and concentration were assessed using an Agilent 2,100
 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA). The
 resulting RNA samples were then pooled and subjected to sequencing on the
 Illumina HiSeq3000 platform in a 150-bp paired-end read format. The raw
 RNA-sequencing (RNA-seq) reads were preprocessed and quantified using the
 featureCounts function in the SubReads package version 1.5.3, with default
 parameters. RNA-seq analysis was conducted on samples
 from 5 mice in the non-perfusion group, 4 mice in the 3-days perfusion
 group, and 5 mice in the 7-days perfusion group of the UPOAO model.
 Additionally, retinas from both the 7-days HIOP experimental eyes and
 bilateral UCCAO eyes were collected (n=5) for analysis.
description: # Transcriptional Responses in a Mouse Model of Silicone Wire Embolization
 Induced Acute Retinal Artery Ischemia and Reperfusion
 [https://doi.org/10.5061/dryad.s1rn8pkhb](https://doi.org/10.5061/dryad.s1rn8pkhb) ## Description of the data and file structure ### Files and variables #### File: Representation\_matrix\_data.rar **Description:**  1. Filename: HIOP_7d      Description: Transcriptome data at 7 days in mice with high intraocular pressure model.     HIOP_1 - HIOP_5: Mice with high intraocular pressure model.  Sham_1 - Sham_5: Sham operation group mice. 2. Filename: UCCAO_7d    Description: Transcriptome data at 7 days in mice with unilateral common carotid artery occlusion model.      UCCAO_1-UCCAO_5: Mice with unilateral common carotid artery occlusion model.  Sham_1 - Sham_5: Sham operation group mice. 3. Filename: UPOAO    Description: Unilateral pterygopalatine ophthalmic artery occlusion model transcriptome data taken immediately after modeling.   UPOAO1-UPOAO_5: Mice with unilateral common carotid artery occlusion model.    Sham_1 - Sham_5: Sham operation group mice. 4. Filename: UPOAO_3d    Description: Unilateral pterygopalatine ophthalmic artery occlusion model: transcriptome data taken from mice 3 days after modeling.   UPOAO_1-UPOAO_4: Mice with unilateral common carotid artery occlusion model.    Sham_1 - Sham_4: Sham operation group mice. 5. Filename: UPOAO_7d    Description: Unilateral pterygopalatine ophthalmic artery occlusion model: transcriptome data taken from mice 7 days after modeling.   UPOAO_1-UPOAO_5: Mice with unilateral common carotid artery occlusion model.    Sham_1 - Sham_5: Sham operation group mice. ## Code/software Data normalization and subsequent processing utilized the 'limma' package in R software (version 4.2.3).