Combined analysis of single cell RNA-Seq and ATAC-Seq data reveals regulatory toggles operating in native and iPS-derived retina

To improve the comparison of the developmental trajectories of native retina (NaR) and iPSC-derived 3D retinal aggregates(3D-RA) , we performed scRNA-Seq of murine NaR and 3D-RA at four matched stages of development: embryonic day (E)13 vs differentiation day (DD)13, postnatal day (P)0 vs DD21, P5 vs DD25 and P9 vs DD29. NaR were dissected from two to 11 C57Bl6 mice (of both sexes) per stage. Mouse 3D-RA were generated from the iPSC Nrl-GFP line. Cells from NaR and OV were dissociated and subjected to droplet-based scRNA-Seq using a 10X Genomics Chromium platform. We obtained sequence information for 21,249 cells from NaR and 16,842 cells from 3D-RA, distributed evenly amongst developmental stages. We generated an average of 74,808 reads per cell, corresponding to 5,940 unique molecular identifiers (UMIs) and 2,471 genes per cell.为优化天然视网膜（native retina, NaR）与诱导多能干细胞（induced pluripotent stem cell, iPSC）来源的三维视网膜聚集体（3D-RA）的发育轨迹对比研究，我们对小鼠天然视网膜及三维视网膜聚集体的4个匹配发育阶段开展了单细胞RNA测序（single-cell RNA sequencing, scRNA-Seq），对应阶段分别为：胚胎天数（E）13与分化天数（DD）13、出生后天数（P）0与DD21、P5与DD25以及P9与DD29。各发育阶段的天然视网膜均取自2至11只C57BL/6小鼠（雌雄兼具）。小鼠三维视网膜聚集体由iPSC Nrl-GFP细胞系构建得到。将天然视网膜与OV来源的细胞解离后，采用10X Genomics Chromium平台开展基于微滴的单细胞RNA测序。本研究共获取天然视网膜来源的21249个细胞与三维视网膜聚集体来源的16842个细胞，这些细胞均匀分布于各发育阶段。我们平均每个细胞测得74808条序列读数，对应每个细胞包含5940个唯一分子标识符（UMIs）与2471个表达基因。