Stabilization competency signature
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE42100 | GEO | 2013/01/01
SECONDARY ACCESSION(S): PRJNA179145
REPOSITORIES: GEO
Similar Datasets
Project description:Comparison of gene expresion profile of 4 SC clones and 4 SI clones at different time points defined a stabilization competency signiture required for successful reprogramming mRNA profilling 4 SI clones at 5 time points, 4 SC clones at 6 time points, and 3 feeder samples.
2013-01-01 | E-GEOD-42100 | biostudies-arrayexpress
Project description:Transcription profiling by high throughput sequencing in gene expresion profile of 4 SC clones and 4 SI clones at different time points defined a stabilization competency signiture
2019-05-14 | E-GEOD-42100 | ExpressionAtlas
Project description:Background: Tomato (Solanum lycopersicum) self-compatibility (SC) is defined as self-pollen tubes that can penetrate their own stigma, elongate in the style and fertilize their own ovules. Self-incompatibility (SI) is defined as self-pollen tubes that are prevented from developing in the style. To determine the influence of gene expression on style self-pollination, a transcriptome-wide comparative analysis of SC and SI tomato unpollinated/pollinated styles was performed using RNA-sequencing (RNA-seq) data. Results: Transcriptome profiles of 24-h unpollination (UP) and self-pollination (P) styles from SC and SI tomato species were generated using high-throughput next generation sequencing. From the comparison of SC self-pollinated and unpollinated styles, 1341 differentially expressed genes (DEGs) were identified, of which 753 were downregulated and 588 were upregulated. From the comparison of SI self-pollinated and unpollinated styles, 804 DEGs were identified, of which 215 were downregulated and 589 were upregulated. Nine gene ontology (GO) terms were enriched significantly in SC and 78 GO terms were enriched significantly in SI. A total of 105 enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified in SC and 80 enriched KEGG pathways were identified in SI, among which “Cysteine and methionine metabolism pathway” and “Plant hormone signal transduction pathway” were significantly enriched in SI. Conclusions: This study is the first global transcriptome-wide comparative analysis of SC and SI tomato unpollinated/pollinated styles. Advanced bioinformatic analysis of DEGs uncovered the pathways of “Cysteine and methionine metabolism” and “Plant hormone signal transduction”, which are likely to play important roles in the control of pollen tubes growth in SI species.
2015-04-09 | GSE67654 | GEO
Project description:Background: Tomato (Solanum lycopersicum) self-compatibility (SC) is defined as self-pollen tubes that can penetrate their own stigma, elongate in the style and fertilize their own ovules. Self-incompatibility (SI) is defined as self-pollen tubes that are prevented from developing in the style. To determine the influence of gene expression on style self-pollination, a transcriptome-wide comparative analysis of SC and SI tomato unpollinated/pollinated styles was performed using RNA-sequencing (RNA-seq) data. Results: Transcriptome profiles of 24-h unpollination (UP) and self-pollination (P) styles from SC and SI tomato species were generated using high-throughput next generation sequencing. From the comparison of SC self-pollinated and unpollinated styles, 1341 differentially expressed genes (DEGs) were identified, of which 753 were downregulated and 588 were upregulated. From the comparison of SI self-pollinated and unpollinated styles, 804 DEGs were identified, of which 215 were downregulated and 589 were upregulated. Nine gene ontology (GO) terms were enriched significantly in SC and 78 GO terms were enriched significantly in SI. A total of 105 enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified in SC and 80 enriched KEGG pathways were identified in SI, among which “Cysteine and methionine metabolism pathway” and “Plant hormone signal transduction pathway” were significantly enriched in SI. Conclusions: This study is the first global transcriptome-wide comparative analysis of SC and SI tomato unpollinated/pollinated styles. Advanced bioinformatic analysis of DEGs uncovered the pathways of “Cysteine and methionine metabolism” and “Plant hormone signal transduction”, which are likely to play important roles in the control of pollen tubes growth in SI species. 24-h unpollination (UP) and self-pollination (P) styles mRNA profiles from SC and SI tomato species were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500 platform.
2015-04-09 | E-GEOD-67654 | biostudies-arrayexpress
Project description:In humans, germline competency and the specification of primordial germ cells (PGCs) are thought to occur in a restricted developmental window during early embryogenesis. Despite the importance of specifying the appropriate number of PGCs for human reproduction, the molecular mechanisms governing PGC formation remain largely unexplored. Here, we compared PGC-like cell (PGCLC) differentiation from 18 independently derived human embryonic stem cell (hESC) lines, and discovered that the expression of primitive streak genes were positively associated with hESC germline competency. Furthermore, we show that chemical inhibition of TGFβ and WNT signaling, which are required for primitive streak formation and CRISPR/Cas9 deletion of Eomesodermin (EOMES), significantly impacts PGCLC differentiation from hESCs. Taken together, our results suggest that human PGC formation involves signaling and transcriptional programs associated with somatic germ layer induction and expression of EOMES.
2018-11-10 | GSE93126 | GEO
Project description:An alternative pluripotent state confers interspecies chimaeric competency
| PRJNA258640 | ENA
Project description:Telencephalic organoids generated from human pluripotent stem cells (hPSC) are emerging as an effective system to study the distinct features of the developing human brain and the underlying causes of many neurological disorders. While progress in organoid technology has been steadily advancing, many challenges remain including rampant batch-to-batch and cell line-to-cell line variability and irreproducibility. Here, we demonstrate that a major contributor to successful cortical organoid production is the manner in which hPSC are maintained prior to differentiation. Optimal results were achieved using fibroblast-feeder-supported hPSC compared to feeder-independent cells, related to differences in their transcriptomic states. Feeder-supported hPSC display elevated activation of diverse TGFβ superfamily signaling pathways and increased expression of genes associated with naïve pluripotency. We further identify combinations of TGFβ-related growth factors that are necessary and together sufficient to impart broad telencephalic organoid competency to feeder-free hPSC and enable reproducible formation of brain structures suitable for disease modeling.
2020-01-01 | GSE140057 | GEO
Project description:Background: The outbreak of coronavirus disease 2019 (COVID-19) poses a considerable health threat to humanity, with potential implications for the ovarian microenvironment remaining uncertain. Methods: Transcriptomic and proteomic analyses of ovarian granulosa cells, along with metabolomic and lipidomic profiling of follicular fluid, were conducted on 17 non-COVID-19 cases and 9 COVID-19 cases. This study received approval from the ethics committee (KYLL-2022-581). Generalized estimating equations model was performed to identify oocyte competency biomarkers. Additionally, cell proliferation, apoptosis, and altered pathways were examined following lentivirus transfection. Methods: Transcriptomic and proteomic analyses of ovarian granulosa cells, along with metabolomic and lipidomic profiling of follicular fluid, were conducted on 17 non-COVID-19 cases and 9 COVID-19 cases. This study received approval from the ethics committee (KYLL-2022-581). Generalized estimating equations model was performed to identify oocyte competency biomarkers. Additionally, cell proliferation, apoptosis, and altered pathways were examined following lentivirus transfection. Conclusions: By integrating untargeted metabolomic and lipidomic features, we identified biomarkers indicative of oocyte competency influenced by COVID-19.
2024-12-25 | GSE282892 | GEO
Project description:I plan to investigate the value of video-based feedback in endoscopic training - specifically, the role of terminal video feedback as compared to usual concurrent feedback on cold snare polypectomy technique in trainees, using Direct Observation of Polypectomy Skills (DOPyS) competency score. I have focused the study on the competency of cold snare polypectomy for subcentimeter polyps. The majority (>75%) of colon polyps are smaller than one centimeter. Cold snare polypectomy has been shown, and recommended by the American Society for Gastrointestinal Endoscopy (ASGE), to be an effective removal technique. However, its widespread use and moreover, its teaching to trainees is lacking. It takes time and resources to learn and teach endoscopic techniques. Our study will hope to identify a mechanism through video-based feedback that could help to improve the translation of the training of polypectomy skills to its actual performance, and to accelerate the learning curve.
| 2241449 | ecrin-mdr-crc