NANOG is required for the long-term establishment of avian somatic reprogrammed cells [duck]
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PROVIDER: PRJNA432456 | ENA |
REPOSITORIES: ENA
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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:NANOG is required for the long-term establishment of avian somatic reprogrammed cells
| PRJNA432454 | ENA
Project description:With the purpose to elucidate the expression changes of host genes of SPF chickens infected with duck-origin H7N9 subtype avian influenza virus at 24 hours post-infection(hpi) and fowl adenovirus-4 at 48 dpi. The spleens of SPF chickens infected with duck-origin H7N9 subtype avian influenza virus and fowl adenovirus-4 were collected and high throughout sequenced. Compared with the control group, there were 2426 differentially expressed genes were obtained in the duck-origin H7N9 subtype avian influenza virus group, including 913 up-regulated genes and 1513 down-regulated genes, and there were 1534 differentially expressed genes were obtained in the fowl adenovirus-4 group, including 632 up-regulated genes and 902 down-regulated genes.
2020-06-03 | GSE151662 | GEO
Project description:While infection of chickens with highly pathogenic avian influenza (HPAI) H5N1 subtypes often leads to complete mortality within 24 to 48 h, infection of ducks in contrast causes mild or no clinical signs. Rapid onsets of fatal disease in chickens, but with no evidence of severe clinical symptoms in ducks, suggest underlying differences in their innate immune mechanisms. To understand the molecular basis for such difference, chicken and duck primary lung cells, infected with a low-pathogenicity avian influenza (LPAI) and two HPAI H5N1 viruses, were subjected to RNA expression profiling using Affymetrix Chicken GeneChip arrays. We used microarrays to analyze the gene expression profiles of primary chicken and duck lung cells infected with H2N3 LPAI and two H5N1 influenza virus subtypes to understand the molecular basis of host susceptibility and resistance. We have identified a set of key genes and pathways that could play an important role in mediating innate host resistance to avian influenza in chickens and ducks.
2014-12-04 | GSE33389 | GEO
Project description:While infection of chickens with highly pathogenic avian influenza (HPAI) H5N1 subtypes often leads to complete mortality within 24 to 48 h, infection of ducks in contrast causes mild or no clinical signs. Rapid onsets of fatal disease in chickens, but with no evidence of severe clinical symptoms in ducks, suggest underlying differences in their innate immune mechanisms. To understand the molecular basis for such difference, chicken and duck primary lung cells, infected with a low-pathogenicity avian influenza (LPAI) and two HPAI H5N1 viruses, were subjected to RNA expression profiling using Affymetrix Chicken GeneChip arrays. We used microarrays to analyze the gene expression profiles of primary chicken and duck lung cells infected with H2N3 LPAI and two H5N1 influenza virus subtypes to understand the molecular basis of host susceptibility and resistance. We have identified a set of key genes and pathways that could play an important role in mediating innate host resistance to avian influenza in chickens and ducks. 24 hours following infection, total RNA from cells was extracted. Replicate RNA samples from each of the virus-infected (H2N3, H5N1 50-92, or H5N1 ty-Ty) or mock-infected chicken and duck cells (4 treatment groups for each species) were used for microarray analysis. Each of the RNA samples was hybridized to one GeneChipM-BM-. Chicken Genome Array (Affymetrix), and a total of 16 array chips were used.
2014-12-04 | E-GEOD-33389 | biostudies-arrayexpress
Project description:Ducks and wild aquatic birds are the natural reservoirs of avian influenza viruses. However, the host proteome response that causes disease in vivo during infection by the highly pathogenic avian influenza (HPAI) H5N1 virus is still not well understood. In the present study, we compared the proteome response in Muscovy duck lung tissue during 3 day of infection with either a highly virulent or an avirulent H5N1 virus. During infection, proteins involved in immune response of neutrophils and size of cells were increased markedly in the lung by the virulent strain, while the avirulent strain evoked a distinct response, characterized by an increase in proteins involved in cell movement, maturation of dendritic cells, adhesion of phagocytes, and immune response of macrophages.
2022-08-22 | PXD002719 | Pride
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 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:In order to elucidate the expression changes of host genes of SPF chickens infected with duck-origin H7N9 subtype avian influenza virus. The lungs of SPF chickens infected with duck-origin H7N9 subtype avian influenza virus were collected and high throughout sequenced. Compared with the control group, there were 740 differentially expressed genes were obtained in infection group, including 602 up-regulated genes and 138 down-regulated genes. The analysis of the GO items showed that the differentially expressed genes were involved in immune responses and inflammatory responses. The results of KEGG analysis showed that 7 pathways were enriched significantly, in those the Toll-like pathway had 11 up-regulated genes, namely IL-6, TLR4, Pik3, IRF7, MD-2, IRF5, MYD88, CD86, STAT1, TLR2, and CCL4. There were 7 up-regulated genes in NOD-like receptor signaling pathway, which were IRF7, CTSB, P2RX7, CYBB, PSTPIP1, HSP90AA1, and NAMPT. In Toll-like signaling pathway，TLR4 was activated by MD-2 after viral infection, and then activated downstream IRF5. At the same time, the NLRP3 inflammasome also played an important role in the process of H7N9 virus infection.
2020-06-03 | GSE151661 | GEO
Project description:Identification of NANOG transcribed factors during the establishment of pluripotency
2018-11-29 | GSE107505 | GEO