NANOG is required for the long-term establishment of avian somatic reprogrammed cells
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ABSTRACT:
PROVIDER: PRJNA432454 | ENA |
REPOSITORIES: ENA
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Project description:NANOG is required for the long-term establishment of avian somatic reprogrammed cells [duck]
| PRJNA432456 | ENA
Project description:Somatic reprogramming, which was first identified in rodents, remains poorly described in non-mammalian species. Here, we generated avian reprogrammed cells by reprogramming of chicken and duck primary embryonic fibroblasts. The efficient generation of long-term proliferating cells depends on the method of delivery of reprogramming factors and the addition of NANOG and LIN28 to the canonical OCT4, SOX2, KLF4, and c-MYC gene combination. The reprogrammed cells were positive for several key pluripotency-associated markers including alkaline phosphatase activity, telomerase activity, SSEA1 expression, and specific cell cycle and epigenetic markers. Upregulated endogenous pluripotency-associated genes included POU5F3 (POUV) and KLF4, whereas cells failed to upregulate NANOG and LIN28A. However, cells showed a tumorigenic propensity when injected into recipient embryos. In conclusion, although the somatic reprogramming process is active in avian primary cells, it needs to be optimized to obtain fully reprogrammed cells with similar properties to those of chicken embryonic stem cells.
| S-EPMC6235669 | biostudies-literature
Project description:Purpose: the goal of this study is to analyse various duck 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 duck primary embryonic fibroblasts (DEF), on blastodermal cells from EGK-X to EG XV embryos (BCs) and reprogrammed cells (R71-2 and R71-5) derived from DEF by somatic reprogramming process. The libraries were prepared using the TruSeq R Stranded mRNA sample preparation kit (Illumina). The paired-end sequencing was performed either on NextSeq 500 or Hiseq 2500 illumina sequencers and controlled by the SeqencingAnalysis 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 was from 30 millions to 40 millions.
2018-04-08 | GSE109969 | GEO
Project description: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.
2018-04-08 | GSE102353 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2018-04-08 | GSE109970 | GEO
Project description:Identification of NANOG transcribed factors during the establishment of pluripotency
2018-11-29 | GSE107505 | GEO
Project description:It has been suggested that the transcription factor Nanog is essential for the establishment of pluripotency during the derivation of embryonic stem (ES) cells and induced pluripotent stem (iPS) cells. However, successful reprogramming to pluripotency with a growing list of divergent transcription factors, at ever increasing efficiencies, suggests that there may be many distinct routes to a pluripotent state. Here, we have investigated whether Nanog is necessary for reprogramming murine fibroblasts under highly efficient conditions using the canonical reprogramming factors Oct4, Sox2, Klf4 and cMyc. In agreement with prior results, the efficiency of reprogramming Nanog-/- fibroblasts was significantly lower than that of control fibroblasts. However, in contrast to previous findings, we were able to reproducibly generate iPS cells from Nanog-/- fibroblasts that effectively contributed to chimeric mice. Thus while Nanog may be an important mediator of reprogramming it is not required for establishing pluripotency in the mouse, even under standard conditions. In order to further evaluate the equivalency of Nanog null iPSC to nanog null ESCs, we have performed RNAseq on two independent nanog null iPSC lines, as well as Nanog Null ESC, WT ESC and iPSCs as well as MEFs. As a negativve control for reprogramming we have analyzed a partially reprogrammed iPSC line. 2-4 biological replicates each of 7 conditions (WT MEFs, WT ESC, WT iPSC, WT partially reprogrammed iPSC (piPS), Nanog null ESC, Nanog null iPSC clone G2 and Nanog null iPSC clone G5)
2014-01-01 | E-GEOD-53212 | biostudies-arrayexpress
Project description:It has been suggested that the transcription factor Nanog is essential for the establishment of pluripotency during the derivation of embryonic stem (ES) cells and induced pluripotent stem (iPS) cells. However, successful reprogramming to pluripotency with a growing list of divergent transcription factors, at ever increasing efficiencies, suggests that there may be many distinct routes to a pluripotent state. Here, we have investigated whether Nanog is necessary for reprogramming murine fibroblasts under highly efficient conditions using the canonical reprogramming factors Oct4, Sox2, Klf4 and cMyc. In agreement with prior results, the efficiency of reprogramming Nanog-/- fibroblasts was significantly lower than that of control fibroblasts. However, in contrast to previous findings, we were able to reproducibly generate iPS cells from Nanog-/- fibroblasts that effectively contributed to chimeric mice. Thus while Nanog may be an important mediator of reprogramming it is not required for establishing pluripotency in the mouse, even under standard conditions. In order to further evaluate the equivalency of Nanog null iPSC to nanog null ESCs, we have performed RNAseq on two independent nanog null iPSC lines, as well as Nanog Null ESC, WT ESC and iPSCs as well as MEFs. As a negativve control for reprogramming we have analyzed a partially reprogrammed iPSC line.
2014-01-01 | GSE53212 | GEO
Project description:NANOG is required for the long-term establishment of avian somatic reprogrammed cells [chicken]
| PRJNA397544 | ENA
Project description:Nanog affects establishment of chromatin marks at zebrafish Zygotic Genome Activation
| PRJNA600508 | ENA