Ena-DATASET-HWGS-11-07-2019-13:56:55:502-589 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001005137 | EGA |
REPOSITORIES: EGA
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Project description:Extracellular vesicles (EVs) released by cells contain mRNAs, miRNAs, lncRNAs, lipids, and proteins, playing crucial roles in cell-cell communication. While full-length mRNA transcripts have been documented in EVs secreted by cancer cells, there are no reports on full transcripts secreted by embryos. Our study aimed to identify EV mRNAs in the culture media of bovine embryos and investigate their roles in embryo-mother communication. Following the isolation of EVs from in-vitro fertilization media samples and RNA sequencing, we identified a full mRNA transcript of DPPA3, known to play an essential role in embryo development. To examine the role of DPPA3 in embryo-mother communication, an in vitro transcribed mRNA of DPPA3 was transfected into bovine endometrial epithelial cells. Transfected and control cells were subsequently analyzed with RNA sequencing and proteomics to assess the effects of DPPA3 on gene expression. A total of 24 genes were found to be upregulated, and one gene was downregulated (FDR < 0.01) following DPPA3 transfection, many with known functions in pregnancy recognition. Proteomic analysis revealed 28 differentially expressed, with 19 upregulated and 15 downregulated. Two proteins, ISG15 and MX1, overlapped with the differentially expressed mRNAs. To mimic the natural transfer of EVs from embryos to endometrial cells, we performed co-culture with day-8 blastocysts or supplemented the cells with embryo-conditioned culture media. DPPA3 presence was detected in endometrial cells exposed to embryo-conditioned media after just 30 minutes. Overall, our study highlights the significant role of EVs in cell-cell communication through mRNA signaling from the embryo to the mother.
2025-01-07 | MSV000096795 | MassIVE
Project description:This experiment examines how increasing stress (sorbitol) can override normal stemness (NS) conditions, which LIF maintains, causing lineage imbalance and otherwise affecting cells in the early embryo. It also compares NS to normal differentiation (ND) (without LIF). D3 are from 8 blastocysts of 129/Sv+/+ strain mice germ line competent 1. No sex is given as these may actually be a product of different sexes of the 8 blastocysts. The D3 cells were obtained for ATCC (American Type Culture Collection). 1. Doetschman TC, Eistetter H, Katz M, Schmidt W, Kemler R. The in vitro development of blastocyst-derived embryonic stem cell lines: formation of visceral yolk sac, blood islands and myocardium. J Embryol Exp Morphol 1985;87:27-45. Rex1 promoter- Red fluorescence protein (RFP) transgenic viable reporter ESC were created and validated previously2. 2. Li Q, Gomez-Lopez N, Drewlo S, et al. Development and Validation of a Rex1-RFP Potency Activity Reporter Assay That Quantifies Stress-Forced Potency Loss in Mouse Embryonic Stem Cells. Stem Cells Dev 2016;25:320-8.
2024-07-19 | GSE237796 | GEO
Project description:Virulent (1874C5) and attenuated (vaccine strain LaryngoVac) strains of infectious laryngotracheitis virus (ILTV) were characterized in vivo for transcript expression via short-read mRNA-Seq and in vitro for transcript and protein expression using full-length cDNA sequencing and high-resolution LC-MS/MS.
2025-02-08 | MSV000097080 | MassIVE
Project description:This experiment examines how increasing stress (sorbitol) can override normal stemness (NS) conditions, which LIF maintains, causing lineage imbalance and otherwise affecting cells in the early embryo. It also compares NS to normal differentiation (ND) (without LIF). D3 are from 8 blastocysts of 129/Sv+/+ strain mice germ line competent 1. No sex is given as these may actually be a product of different sexes of the 8 blastocysts. The D3 cells were obtained for ATCC (American Type Culture Collection). 1. Doetschman TC, Eistetter H, Katz M, Schmidt W, Kemler R. The in vitro development of blastocyst-derived embryonic stem cell lines: formation of visceral yolk sac, blood islands and myocardium. J Embryol Exp Morphol 1985;87:27-45. Rex1 promoter- Red fluorescence protein (RFP) transgenic viable reporter ESC were created and validated previously2. 2. Li Q, Gomez-Lopez N, Drewlo S, et al. Development and Validation of a Rex1-RFP Potency Activity Reporter Assay That Quantifies Stress-Forced Potency Loss in Mouse Embryonic Stem Cells. Stem Cells Dev 2016;25:320-8.
2024-10-16 | GSE245532 | GEO
Project description:Extracellular vesicles (EVs) released by cells contain mRNAs, miRNAs, lncRNAs, lipids, and proteins, playing crucial roles in cell-cell communication. While full-length mRNA transcripts have been documented in EVs secreted by cancer cells, there are no reports on full transcripts secreted by embryos. Our study aimed to identify extracellular vesicle mRNAs in the culture media of bovine embryos and investigate their roles in embryo-mother communication. Following the isolation of EVs from in-vitro fertilization media samples and RNA sequencing, we identified full mRNA transcripts of three genes: SLBP2, ACCSL, and DPPA3. We selected DPPA3 for further investigation. To examine the role of DPPA3 in embryo-mother communication, an in vitro transcribed mRNA of DPPA3 was transfected into bovine endometrial epithelial cells. Transfected and control cells were subsequently analyzed for RNA sequencing to assess the effects of DPPA3 on gene expression. A total of 24 genes were found to be upregulated, and one gene was downregulated (FDR < 0.01) following DPPA3 transfection. Among the 18 annotated genes, 17 have known functions in pregnancy recognition in ruminants or have been previously identified as upregulated in pregnant animals. In addition to RNA sequencing, transfected and control cells underwent proteomic analysis. A total of 34 proteins were differentially expressed (FDR < 0.01, p < 0.05, fold change > 1.5), with 19 upregulated and 15 downregulated. Two proteins, ISG15 and MX1, overlapped with the differentially expressed mRNAs. To mimic the natural transfer of EVs from embryos to endometrial cells, we performed co-culture of day 8 blastocysts or supplemented the cells with embryo-conditioned culture media. DPPA3 expression was detected in endometrial cells exposed to embryo-conditioned media after just 30 minutes, with slight upregulation of ISG15 and MX1 also observed. The expression of these classic interferon-stimulated genes in endometrial cells increased from 0.5 to 10 hours when exposed to blastocysts or embryo-conditioned media. Overall, these results demonstrate that DPPA3 mRNA secreted from embryos may play a role in early embryo-mother communication and maternal recognition of pregnancy prior to major interferon tau secretion. Importantly, our study highlights the significant role of EVs in cell-cell communication through mRNA signaling from the embryo to the mother.
2025-06-04 | GSE269049 | GEO
Project description:Full-Length cDNA transcriptome (Iso-Seq) data sequenced on the PacBio Sequel system using 2.1 chemistry. Multiplexed cDNA library of 12 samples (3 tissues x 4 strains). Tissues: root, embryo, endosperm. Strains: B73, Ki11, B73xKi11, Ki11xB73.
2020-02-25 | E-MTAB-7837 | biostudies-arrayexpress
Project description:Our previous study using nude rats revealed that the parental JDCaP xenografts predominantly expressed full-length androgen receptor (AR) whereas the relapsed JDCaP xenografts after castration acquired AR splice variants including AR-V7 and ARv567es. To understand molecular mechanisms underlying the acquisition of AR splice variants in the JDCaP model, we performed microarray analysis using RNA samples of the xenografts without castration (Parent), the relapsed xenografts overexpressing full-length AR and AR-V7 (ARhiV7hi), and the relapsed xenografts expressing ARv567es (ARv567es).
2016-12-25 | GSE90922 | GEO
Project description:Using a highly efficient and strand-specific RNA-seq method combined with a highly accurate and robust algorithm and tool we developed, TruHMM for assembling full-length transcriptomes, to profile the transcriptome of E.coli K12 under different culture conditions and growth phases, we showed that the dynamic transcriptome structures appears to be culture condition and growth phases dependent.
2013-06-21 | GSE48151 | GEO
Project description:Effect of embryo in vitro culture on mESC transcriptome.
| PRJNA269159 | ENA