Bulk RNA sequencing analysis of developing human induced pluripotent cell-derived retinal organoids.

Bulk RNA sequencing analysis of developing human induced pluripotent cell-derived retinal organoids.

Scientific data (2022-12-10)

Devansh Agarwal, Rian Kuhns, Christos N Dimitriou, Emmalyn Barlow, Karl J Wahlin, Ray A Enke

ABSTRACT

Retinogenesis involves the transformation of the anterior developing brain into organized retinal lamellae coordinated by intricate gene signalling networks. This complex process has been investigated in several model organisms such as birds, fish, mammals and amphibians, yet many facets of retinal development are different in humans and remain unexplored. In this regard, human pluripotent stem cell (hPSC)-derived 3D retinal organoids and Next Generation Sequencing (NGS) have emerged as key technologies that have facilitated the discovery of previously unknown details about cell fate specification and gene regulation in the retina. Here we utilized hPSCs integrated with fluorescent reporter genes (SIX6-p2A-eGFP/CRX-p2A-h2b-mRuby3) to generate retinal organoids and carry out bulk RNA sequencing of samples encompassing the majority of retinogenesis (D0-D280). This data set will serve as a valuable reference for the vision research community to characterize differentially expressed genes in the developing human eye.

MATERIALS

Product Number

Brand

Product Description

B0560

Sigma-Aldrich

(−)-Blebbistatin, solid, synthetic

565770

Sigma-Aldrich

γ-Secretase Inhibitor IX, Gamma-Secretase Inhibitor IX - CAS 208255-80-5, is a cell-permeable inhibitor of γ-secretase (Aβtotal IC₅₀ = 115 nM, Aβ42 IC₅₀ = 200 nM).

A6964

Sigma-Aldrich

Accutase^® solution, sterile-filtered, suitable for cell culture

566660

Sigma-Aldrich

Smoothened Agonist, SAG, A cell-permeable Smoothened Agonist, SAG, CAS 364590-63-6, modulates the coupling of Smo with its downstream effector by interacting with the Smo heptahelical domain (K_D = 59 nM).