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NANOG is required for the long-term establishment of avian somatic reprogrammed cells [chicken]

ABSTRACT: Purpose: the goal of this study is to analyse various chicken stem cell lines and to compare them with both primary somatic fibroblasts and blastodermal cells derived from pre-gastrulating embryos Methods: NGS RNA-sequencing was performed on chicken primary embryonic fibroblasts (CEF), embryonic stem cells (cESC), on blastodermal cells of EGK-X EGK-XII stages embryos (BCs), long term in vitro cultured primordial germ cells (PGCs) as specific chicken stem cells and reprogrammed cells (1A, 1D, 3E, 3F) derived from CEF by somatic reprogramming process. The librairies were prepared using the TruSeq R Stranded mRNA sample preparation kit (Illumina). The paired-end sequencing was performed on the NextSeq 500 sequencer (Illumina) and controlled by the Seqencing Analysis viewer software (Illumina). The quality control of the Sample-ID.fastq files was performed with the FasQC software (Babraham Institute). Results: the total number of reads ranges from was of 80 millions to 145 millions.

ORGANISM(S): Gallus gallus

PROVIDER: GSE102353 | GEO | 2018/04/08

REPOSITORIES: GEO

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Project description:Eyal-Giladi and Kochav stage X (EGK.X) blastoderm mostly consists undifferentiated progenitor (pluripotent) cells that have the potency to differentiate into all cell types. Analyzing the transcriptional programs of blastoderm is critical to understand the molecular mechanisms that underlie the developmental fate of early embryos, and practical application of blastoderm-derived pluripotent cells, including ESC. Primordial germ cells (PGC) are also undifferentiated progenitor cells that later differentiate into male and female germ cells. Analyzing the transcriptional programs of PGC is critical to understand the molecular mechanisms that underlie the developmental fate of early germ cells, and practical application of PGC in generating transgenic chickens. Therefore, we performed whole-transcriptome sequencing (WTS) in the chicken EGK.X blastoderm and PGCs together with the chicken embryonic fibroblasts (CEF, as a reference sample). CEF are differentiated and an abundant somatic cells. The generated WTS data of CEF, EGK.X blastoderm and PGC are rich resources to utilize for various focused research. As a first focused research, we utilized the generated WTS data for analyzing the expression profiling of DNA repair and apoptosis pathway genes in EGK.X blastoderm and PGC compared with CEF. DNA is the fundamental unit of inheritance and is susceptible to damage by various exogenous and endogenous sources. When the DNA is damaged, the cell sense the nature of damage through multiple surveillance mechanisms and select an appropriate DNA repair pathway to repair the damage and avoid passing the damage to a progeny of cells. When the cell fails to repair DNA damage, cell cycle progression is halted and apoptosis is initiated. Despite several genes are involved in five major DNA repair pathways and two major apoptosis pathways, a comprehensive understanding on the expression of those genes are not well-understood in chicken tissues. Through WTS analysis in CEF, stage X blastoderm and PGC, we identified that most of the DNA repair pathway genes were expressed more high in blastoderm and high in PGC than CEF. At the other hand, most of the apoptosis pathway genes were expressed low in blastoderm and PGC than CEF.

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NANOG is required for the long-term establishment of avian somatic reprogrammed cells [chicken]

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