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

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.

Transcriptome dataset of Caenorhabditis elegans responses to varied microbial pathogens

“…Libraries for cDNA samples were sequenced using the Illumina HiSeq 4000 platform yielding 22-34.4 million 150 bp paired end (PE) sequence reads per sample ( Table 1 ). Raw sequence data was returned and analyzed using a previously established open access bioinformatics package ( Fig 1 a) [14] .…”

Transcriptome and Metabolome Analyses Reveal the Mechanism of Corpus Luteum Cyst Formation in Pigs

“…We obtained 57,229,092, 39,761,374, and 40,244,178 raw reads from the corpus luteum samples, and 49,227,446, 46,621,552, and 57,313,272 raw reads from the corpus luteum cysts (Figure 2A). The raw data were quality tested using FastQC [15]. For all of the samples, the Q20 values were >95%, indicating that the sequencing data were of reliable quality with a low error rate.…”

Organoid Models and Next-Generation Sequencing for Bone Marrow and Related Disorders

“…Once the models can partially mimic the physiological conditions, NGS can be used to confirm the genetic landscape of the physiological conditions and explore and predict therapeutic responses. The combination of organoid and NGS technology has already been attempted to investigate breast cancer organoids [128] and retinal organoids [129]. As quoted by the creators of 'OrganoidDB', similar platforms could not only 'facilitate a better understanding of organoids' but additionally seek to improve current organoid culture protocols to model organoids that 'fully recapitulate the structure of the modelled organs' [96].…”