Bulk RNA-seq time-course of human iPSc differentiation to thymic epithelial progenitors

Bulk RNA-seq was performed across a time-course of human iPSc differentiation toward thymic epithelial progenitors (TEPs). Twenty-nine experimental libraries spanning eleven time-points (days 0, 1, 2, 3, 7, 9, 10, 14, 15, 17, 22) plus four primary thymic epithelial cell (TEC) controls revealed progressive down-regulation of pluripotency genes and stepwise activation of transcriptional modules corresponding to anterior endoderm, third pharyngeal pouch endoderm, and thymic epithelial fate. Overall design: Human induced pluripotent stem cells (iPSc; line LON71) were differentiated toward thymic epithelial progenitors (TEPs) using our defined iPSc-to-TEP protocol. RNA was extracted with the RNeasy Micro Kit (Qiagen) at eleven time-points: D0 (n = 3), D1 (n = 1), D2 (n = 1), D3 (n = 4), D7 (n = 5), D9 (n = 6), D10 (n = 4), D14 (n = 2), D15 (n = 1), D17 (n = 1), D22 (n = 1). Four primary pediatric thymic epithelial cell (TEC) samples served as references. All samples were sequenced using 3' RNA-seq (DGE-seq).