RNA sequencing analysis of the developing chicken retina

Abstract

RNA sequencing transcriptome analysis using massively parallel next generation sequencing technology provides the capability to understand global changes in gene expression throughout a range of tissue samples. Development of the vertebrate retina requires complex temporal orchestration of transcriptional activation and repression. The chicken embryo (Gallus gallus) is a classic model system for studying developmental biology and retinogenesis. Existing retinal transcriptome projects have been critical to the vision research community for studying aspects of murine and human retinogenesis, however, there are currently no publicly available data sets describing the developing chicken retinal transcriptome. Here we used Illumina RNA sequencing (RNA-seq) analysis to characterize the mRNA transcriptome of the developing chicken retina in an effort to identify genes critical for retinal development in this important model organism. These data will be valuable to the vision research community for characterizing global changes in gene expression between ocular tissues and critical developmental time points during retinogenesis in the chicken retina.

Whole genome DNA methylation sequencing of the chicken retina, cornea and brain

“…Chicken embryos were harvested and euthanized at specified days incubated as previously described 9 . Briefly, embryos were decapitated and eyes were enucleated.…”

“…Isolated corneas and whole brain extracts were saved for subsequent DNA extraction. Histological preparation of eyecups was conducted as previously described 9 . Briefly, eyecups were fixed in 4% paraformaldehyde in 1× PBS for 25 min on ice, equilibrated in 25% sucrose in 1× PBS, and transferred into a 2:1 mixture of 25% sucrose:OCT compound (Electron Microscopy Sciences) on ice for 30 min prior to flash freezing in the same solution in Tissue-Tek Cryomold (Sakura Finetek) and stored in −80 °C.…”

“…Progenitor cells yet to exit the cell cycle, as well as each of these specialized retinal cell types are known to express developmental and cell type-specific genes 7 . RNA-sequencing transcriptome data have recently become available to dissect global changes in gene expression during chick retinal development 8 , 9 . Currently, however, there are no publicly available data sets characterizing epigenetic modifications of the genome in the developing chicken retina.…”

The Effects of Snake Venom (Bitis arietans) on Embryonic Development

“…The lens does not have to be present for the regeneration, and the regenerating tissue develops faster than normal [14]. The chicken model is used in the vision research community to study human retinogenesis and develop new ways to battle human blindness and eye disease by allowing scientists an insight into the complex regulatory network of neurons and glial cells [15]. In America, diabetic retinopathy is the leading cause of blindness amongst over 40-year-olds [16] with all type 1 diabetes developing DR and more than 60% with type 2 [17].…”

Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

“…A global expression atlas for the chicken transcriptome was created by combining our immune-related data with 20 publicly archived RNA-seq datasets. Some were collated by the Avian RNA-seq Consortium [41], while others are drawn from a diverse range of existing publications, including studies that characterised the genetic basis of retinogenesis [42], the genetic determinants of meat tenderness [43], the morphological diversity of skin appendages [44], visceral fat metabolism [45], the transition between laying and brooding phases [46], the effect of heat stress upon pituitary development [47] and spleen function [48], the pathways involved in avian influenza resistance [49], the role of lncRNAs in the development of muscle [50], liver and adipose [51], and the transcriptional landscape of mRNA editing [52]. In total, 279 RNA-seq libraries were obtained, representing 48 distinct tissue and cell types at developmental stages spanning early embryonic (5 days) to mature adult (70 weeks post-hatching).…”