Ontology highlight
ABSTRACT:
PROVIDER: PRJNA743165 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Here, we produced a set of interspecific F1 triploid hybrid plants between Oryza sativa, ssp. japonica (2nâ=â2xâ=â24, genome AA) and the tetraploid form of O. punctata (2nâ=â4xâ=â48, genome, BBCC), and conducted RNA-seq transcriptome profiling of the hybrids and their exact parental plants. We analyzed both homeolog expression bias and overall gene expression level difference in the hybrids relative to the in silico âhybridsâ (parental mixtures). We found that approximately 16% (2,541) of the 16,112 expressed genes in leaf tissue of the F1 hybrids showed nonadditive expression, which were specifically enriched in photosynthesis-related pathways. Interestingly, changes in the maternal homeolog expression, including non-stochastic silencing, were the major causes for altered homeolog expression partitioning in the F1 hybrids. Our findings have provided further insights into the transcriptome response to interspecific hybridization and heterosis.
2015-05-02 | E-MTAB-4225 | biostudies-arrayexpress
Project description:The aim of this experiment is to characterize the genome composition of the two hybrids IF6 and MR25. IF6 and MR25 are hybrids among S.cerevisiae and S. kudriavzevii. The hybridization of the genome extraction with the microarray was at 65C, under this condition only S. cerevisiae genes can hybridize. In this case we are only studying the genome composition of S. cerevisiae parental in the hybrids. The study of S. kudriavzevii parental genome was done by other methods.
2012-11-05 | E-MEXP-3375 | biostudies-arrayexpress
Project description:The goal of this study is to compare the mouse strains C57BL/6 and CAST/EiJ and their hybrids of forward and reverse mating (F1i and F1r respectively) in behavioral, molecular and electrophysiological level. We examine the effects of parental genotypes on the offspring phenotypes using behavioral studies, electrophysiology and RNA-seq. We show that despite having the same genome, the F1i and the F1r hybrids display different phenotypes, and this may be due to having opposite parental sources of the same genome.
2021-10-31 | GSE160575 | GEO
Project description:Evasion from immunity is a major obstacle for achievement of successful cancer immunotherapy. Hybrids derived from cell-cell fusion is a theory associated with tumor heterogeneity and progression by conferring novel properties to tumor cells, such as drug resistance or metastatic capacity; however, its impact on immune evasion remains still unknown. Here, we investigated the potency of hybrids in immune evasion using tumor-macrophage hybrids. Hybrids were established by co-culture of a melanoma cell line, A375 and type 2 macrophages. The hybrids showed higher migration ability and higher tumorigenicity than those of the parental melanoma cells. We found that the hybrids were less sensitive to T cell receptor (TCR) specific for NY-ESO-1 transduced T cells (TCR-T cells) than parental melanoma cells, although hybrids and parental melanoma cells showed equivalent NY-ESO-1 expression. An in vitro tumor heterogeneity model revealed that TCR-T cells preferentially killed parental cells than hybrids and the survival rate of hybrids were higher than that in parental cells indicating hybrids evade from killing by TCR-T cells efficiently. A single cell analysis data set revealed that a few macrophage cells expressed melanoma differentiation antigens including gp100, MART-1 and tyrosinase, indicating hybrids exist in primary melanoma, and number of potential hybrids were corelated with poorer response to immune checkpoint blockade. These results provide evidence that melanoma-macrophage fusion has a role in tumor heterogeneity and immune evasion.
2023-05-04 | GSE210578 | GEO
Project description:The phenomenon of heterosis describes the increased agronomic performance of heterozygous F1-plants compared to their homozygous parental inbred plants. Heterosis is already manifested during the early stages of root development in maize. The goal of this study was to identify non-additive gene expression in primary roots of maize hybrids compared to the average expression levels of their parental inbred lines. To achieve this goal a two step strategy was selected. First, a microarray preselection of non-additively expressed candidate genes was performed. Subsequently, gene expression levels in a subset of genes were determined via high throughput qRT-PCR experiments. Initial microarray experiments identified 1941 non-redundant genes which displayed non-additive gene expression in at least one of the twelve analyzed hybrids compared to the midparent value of their parental inbred lines. Comparison of these 1941 genes with non-additively expressed genes identified in maize shoot apical meristems via the same experimental procedure in the same genotypes revealed significantly less overlap than expected by pure chance supporting. This supports the notion of organ specific patterns of non-additively expressed genes. qRT-PCR analyses of 64 of the 1941 non-additively expressed genes in four different hybrids revealed that the majority of non-additively expressed genes were expressed between the high and low parent expression values and only a small fraction of genes was expressed below low or above high parent levels. Subsequently, 22 of the 64 genes that displayed non-additive expression in all four hybrids were analyzed in twelve hybrids that were generated from four inbred lines. Among those genes a superoxide dismutase 2 was expressed significantly above the midparent value in all twelve hybrids and might thus play a protective role in antioxidative defense in the primary root of maize hybrids. These findings are consistent with the hypothesis that global expression trends but also the consistent differential expression of key genes might be relevant during the organ-specific manifestation of heterosis. Keywords: Comparative genomic hybridization
2008-02-16 | GSE10539 | GEO
Project description:Rose (Rosa hybrida L.) is a major cut flowers in the world. Studying the molecular mechanism of auxin regulation in growth is of great significance for enhancing the understanding of the growth and development processes of rose and informing accurate exogenous auxin application in rose production. However, the response mechanism of rose to miRNA-mediated auxin signal transduction is unclear. In this study, rose plants were treated with IAA, and 75 known miRNAs and 168 novel miRNAs were identified by small RNA sequencing. Among them, 19 known miRNAs and 42 miRNAs were differentially expressed. Many differential miRNAs demonstrated staged responses to auxin treatment. The targeted relationship between miRNA and key transcription factors regulated by auxin in rose was analyzed, and the target genes in the ARF family and AUX/IAA family were screened. By using quantitative real-time PCR(qRT-PCR) to verify the expression patterns of the miRNA regulating the auxin signal transduction pathway and its target gene, we found that miR156a, miR160a, miR164a, miR167d, miR396b-3p, novel_miR_189, novel_miR_74, novel_miR_8, and novel_miR_207 interacted negatively with the ARF family, and miR390a-3p and novel_miR_101 interacted negatively with the AUX/IAA family. These results provide a theoretical basis for further studies on the auxin regulatory mechanisms in rose.
2023-02-28 | GSE225844 | GEO
Project description:Protein expression profiling of root tip of tobacco hybrids and parental was analyzed by data indpendent acquisition proteomics
2021-09-18 | PXD028624 | iProX