Microarray analysis of mouse retinal organoids

ES/iPS-retinal sheet transplantation, which supplies photoreceptors as well as other retinal cells, has been shown able to restore visual function in mice with end-stage retinal degeneration. Here, we introduce a novel type of genetically engineered mouse ES/iPS-retinal sheet with reduced numbers of secondary retinal neurons but intact photoreceptor cell layer structure (Bhlhb4 knockout and Islet1 knockout). We show that this KO grafts can differentiate into retinal organoids with similar potency as wildtype retinal organoids. The data set contains data from 3 cell  lines: wildtype (WT, specified as ‘NCT’), B4KO (Bhlhb4 knock-out), and Isl1KO(Islet-1 knockout) across 3 differential days (DDs, DD10, DD16, and DD23) along the early differentiation of retinal tissue. We compared the expression pattern of retinal organoids that were genetically engineered to reduce the number of bipolar cell numbers. The data set contains data from 3 cell  lines: wildtype (WT, specified as ‘NCT’), B4KO (Bhlhb4 knock-out), and Isl1KO(Islet-1 knockout) across 3 differentian days (DDs, DD10, DD16, and DD23) RNA was prepared using TRIZOL reagent (thermo fisher), following manufacturers instructions. For each sample, 5 retinal organoids were aggregated to ensure enough RNA was obtained. Extracted RNA was purified using QIAGEN RNeasy Micro Kit and quantified using a NanoDrop-1000 spectrophotometer and  the quality of purified RNA was monitored using Agilent 2100 Bioanalyzer.