{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Petros Moustardas"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16492"],"description":["Cornea transcriptomic analysis in a mouse model of slowly progressing aniridia-associated keratopathy (AAK) the heterozygous 129S1.Cg-Pax6Sey/Mmmh strain on the 129S1/SvImJ background (MMRRC stock #050624-MU)(4, 5). The Pax6 mutation of this model is a spontaneous point mutation in exon 8 of the Pax6 gene (G to T substitution), leading to a premature stop codon. Mice were treated with 10 μM duloxetine eyedrops (samples named Het-Dul) or vehicle (Samples named Het-Veh) twice daily, for 90 days. The experimental design also included non-mutant, WT mouse eyes that were either administered with the same regimen of duloxetine (samples named Wt-Dul) or untouched (Samples names Wt-Ctrl)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - At the end of the experiment, mice were euthanized for tissue extraction. Eyes were enucleated and immediately rinsed in ice-cold PBS. Cornea tissue was dissected under a stereoscope and placed in RNA later solution, where it was stored at -80 degrees C until processing for RNA extraction.","Nucleic Acid Extraction - RNA extraction was performed using the GeneJET RNA Purification Kit (Life Technologies, K0731) according to the manufacturer’s instructions, with a final elution volume of 20 μL. RNA concentration was measured using the NanoDrop One spectrophotometer (Thermo Fisher), while RNA quality was assessed with the Agilent 2100 Bioanalyzer and High Sensitivity RNA Analysis Kit, ensuring all samples had a RIN >8.8. For high-throughput transcriptome analysis, the GeneChip WT Plus Reagent Kit (Thermo Fisher) was used in the MO 2.0 array system with 100 ng of total RNA per reaction, following the kit’s protocol.","Scaning - According to the Affymetrix GeneChip microarray manufacturer protocol","Labeling - According to the Affymetrix GeneChip microarray manufacturer protocol","Hybridization - According to the Affymetrix GeneChip microarray manufacturer protocol"],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"data_protocol":["Data Transformation - GeneChip scan analysis was performed using the Transcriptome Analysis Console (TAC v4.0.3.14, Applied Biosystems) loaded with the MO 2.0 library. Besides the conversion of optical data into transcript quantification, TAC was used to perform Quality Control, principal component analysis (default settings), groupwise per-protein t-tests (threshold p value < 0,05 and |FC| >1.4) followed by WikiPathways pathway enrichment analysis. All raw data were exported into spreadsheets for further bioinformatics analysis with the STRING Protein- Protein Interaction Networks Functional Enrichment Analysis tool (STRING v.12.0)."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"pubmed_abstract":["Aniridia is a rare congenital condition of abnormal eye development arising principally from heterozygous mutation of the PAX6 gene. Among the multiple complications arising in the eye, aniridia-associated keratopathy (AAK) is a severe vision-impairing condition of the cornea associated with a progressive limbal stem cell deficiency that lacks suitable treatment options. Current mouse models of aniridia do not accurately represent the onset and progression dynamics of human AAK, hindering therapy development. Here, we performed deep phenotyping of a haploinsufficient Pax6+/- small-eye (Sey) mouse model on the 129S1/SvImJ background, which exhibits key features of mild presentation at birth and progressive AAK with aging, mimicking human disease. The model exhibits a slowly progressing AAK phenotype and provides insights into the disease, including disturbed basal epithelial cell organization, function, and marker expression; persistent postnatal lymphangiogenesis; disrupted corneal innervation patterns; and persisting yet altered limbal stem cell marker expression with age. The model recapitulates many of the known features of human disease, enabling investigation of underlying disease mechanisms and, importantly, access to a well-defined temporal window for evaluating future therapeutics."],"study_type":["transcription profiling by array"],"species":["Mus musculus"],"pubmed_title":["A human-like model of aniridia-associated keratopathy for mechanistic and therapeutic studies","Transcriptomic analysis in a model of aniridia-associated keratopathy for target discovery and evaluation of duloxetine therapy"],"pubmed_authors":["Dina Javidjam, Petros Moustradas, Ava Dashti, Daniel Aberdam, Arnaud Schweitzer-Chaput, Salvatore Cisternino, Dominique Bremond-Gignac, Neil Lagali","Dina Javidjam, Petros Moustardas, Mojdeh Abbasi, Ava Dashti, Yedizza Rautavaara, Neil Lagali","Petros Moustardas"],"additional_accession":[]},"is_claimable":false,"name":"Mouse cornea trasnciptomics: Pax6-sey mutation (Aniridia model) and Duloxetine administration - Affymetrix GeneChip Mouse Gene 2.0 ST Array (MoGene-2_0-st) in -","description":"Cornea transcriptomic analysis in a mouse model of slowly progressing aniridia-associated keratopathy (AAK) the heterozygous 129S1.Cg-Pax6Sey/Mmmh strain on the 129S1/SvImJ background (MMRRC stock #050624-MU)(4, 5). The Pax6 mutation of this model is a spontaneous point mutation in exon 8 of the Pax6 gene (G to T substitution), leading to a premature stop codon. Mice were treated with 10 μM duloxetine eyedrops (samples named Het-Dul) or vehicle (Samples named Het-Veh) twice daily, for 90 days. The experimental design also included non-mutant, WT mouse eyes that were either administered with the same regimen of duloxetine (samples named Wt-Dul) or untouched (Samples names Wt-Ctrl).","dates":{"release":"2026-01-30T00:00:00Z","modification":"2026-05-27T14:32:23.322Z","creation":"2025-12-24T16:08:52.075Z"},"accession":"E-MTAB-16492","cross_references":{"pubmed":["39625791"],"EFO":["EFO_0002768","EFO_0002944","EFO_0003814","EFO_0003813","EFO_0005518","EFO_0003816","EFO_0003815"],"doi":["10.1172/jci.insight.183965"]}}