Scombridae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA956065 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:A phylogenetic analysis of seven different species (human, mouse, rat, worm, fly, yeast, and plant) utilizing all (541) basic helix-loop-helix (bHLH) genes identified, including expressed sequence tags (EST), was performed. A super-tree involving six clades and a structural categorization involving the entire coding sequence was established. A nomenclature was developed based on clade distribution to discuss the functional and ancestral relationships of all the genes. The position/location of specific genes on the phylogenetic tree in relation to known bHLH factors allows for predictions of the potential functions of uncharacterized bHLH factors, including EST's. A genomic analysis using microarrays for four different mouse cell types (i.e. Sertoli, Schwann, thymic, and muscle) was performed and considered all known bHLH family members on the microarray for comparison. Cell-specific groups of bHLH genes helped clarify those bHLH genes potentially involved in cell specific differentiation. This phylogenetic and genomic analysis of the bHLH gene family has revealed unique aspects of the evolution and functional relationships of the different genes in the bHLH gene family. PMID: 18557763 We used microarrays to determine bHLH expression in 20d rat Sertoli cells. RNA samples from two control groups (Sertoli cells cultured for 72 h) are compared to two treated groups (Sertoli cells cultured for 72 h with cAMP).
2010-02-21 | E-GEOD-20259 | biostudies-arrayexpress
Project description:A phylogenetic analysis of seven different species (human, mouse, rat, worm, fly, yeast, and plant) utilizing all (541) basic helix-loop-helix (bHLH) genes identified, including expressed sequence tags (EST), was performed. A super-tree involving six clades and a structural categorization involving the entire coding sequence was established. A nomenclature was developed based on clade distribution to discuss the functional and ancestral relationships of all the genes. The position/location of specific genes on the phylogenetic tree in relation to known bHLH factors allows for predictions of the potential functions of uncharacterized bHLH factors, including EST's. A genomic analysis using microarrays for four different mouse cell types (i.e. Sertoli, Schwann, thymic, and muscle) was performed and considered all known bHLH family members on the microarray for comparison. Cell-specific groups of bHLH genes helped clarify those bHLH genes potentially involved in cell specific differentiation. This phylogenetic and genomic analysis of the bHLH gene family has revealed unique aspects of the evolution and functional relationships of the different genes in the bHLH gene family. PMID: 18557763 We used microarrays to determine bHLH expression in 20d rat Sertoli cells.
2010-02-11 | GSE20259 | GEO
Project description:Phylogenetic relationships in Apocynaceae based on nuclear PHYA and plastid trnL-F sequences
| PRJEB24297 | ENA
Project description:Phylogenetic relationships in Apocynaceae based on nuclear PHYA and plastid trnL-F sequences
| PRJEB24389 | ENA
Project description:Phylogenetic relationships in Apocynaceae based on nuclear PHYA and plastid trnL-F sequences
| PRJEB24390 | ENA
Project description:Systematics of Vriesea (Bromeliaceae): phylogenetic relationships based on nuclear gene and partial plastome sequences
| PRJNA554504 | ENA
Project description:Breast cancer is among the most common malignancies and the leading cause of cancer-related deaths in women. SRSF1 proteins belong to an important splicing factor (SF) family and bind to different splicing regulatory elements (SREs) to promote or inhibit splicing. Cyperotundone (CYT) is the major bioactive component of sedge and reported to exhibit multiple biological functions. This study aimed to investigate the effects of CYT on breast cancer drug resistance and to explore the molecular mechanisms. CYT significantly suppressed the in vitro and in vivo growth of BC cells without affect the normal cells, induced cell apoptosis, and inhibited the migration and invasion of drug-resistant BC. In comparison with the mono treatment with CYT, combination of CYT and doxrubicin (Dox) enhanced the effects. CYT treatment regulated the RNA and protein levels of epithelial mesenchymal transition (EMT) biomarkers, suppressed the sphere formation ability and expression of cancer stem cell biomarkers in drug resistant BC cells. Results from transcriptome sequencing analysis and experiments identified significantly decreased SRSF1 level in drug resistant cells after CYT treatment. Knockdown of SRSF1 significantly decreased expression of full-length MYO1B protein in drug-resistant BC cells. Overexpression of SRSF1 and MYO1B revered the inhibitory effects of CYT. In conclusion, CYT repressed the growth and metastasis of BC cells and recovered drug sensitivity, via regulating the alternative splicing of RNAs.
2025-04-09 | GSE291469 | GEO
Project description:Analysis of leaves of wild-type and rice COI mutants treated with methyl jasmonate (MeJA). Results provide the role of rice COI on response to jasmonic acid.
2022-06-11 | GSE205750 | GEO
Project description:The Danioninae subfamily of teleost fishes boasts up to four hundred distinct species that have evolved to display a stunning diversity of morphological forms. Here we use newly assembled genome sequences of four laboratory and wild zebrafish strains as well as eleven species of the Danio and Danionella genera to explore their phylogenetic history and the genetic basis of pigment pattern diversification. Phylogenomic analyses uncover extensive introgression and incomplete lineage sorting that have obscured phylogenetic relationships within Danio and corroborate an ancient hybrid origin of zebrafish. Whereas D. rerio inherited ancestral horizontal stripes, relatives repeatedly evolved spots and vertical bars. Interspecific complementation tests reveal functional divergence of the adhesion molecule gene igsf11 and the gap junction gene gja5b between the striped zebrafish and Danio species with divergent patterns. Comparative genomic and transcriptomic analyses suggest that protein and regulatory evolution have accompanied pigment pattern diversification. Our analyses elucidate complex genetic changes underlying the phylogenetic history and morphological diversification in the Danio genus. Resolved phylogenetic relationships, available genome assemblies, transcriptomes, and genetic tractability establish Danio fish species as excellent models for biomedical research in vertebrates.
2026-02-11 | GSE319137 | GEO
Project description:<p>Intratumoral genetic heterogeneity has been characterized across cancers by genome sequencing of bulk tumors, including chronic lymphocytic leukemia (CLL). In order to more accurately identify subclones, define phylogenetic relationships, and probe genotype-phenotype relationships, we developed methods for targeted mutation detection in DNA and RNA isolated from thousands of single cells from five CLL samples. By clearly resolving phylogenic relationships, we uncovered mutated LCP1 and WNK1 as novel CLL drivers, supported by functional evidence demonstrating their impact on CLL pathways. Integrative analysis of somatic mutations with transcriptional states prompts the idea that convergent evolution generates phenotypically similar cells in distinct genetic branches, thus creating a cohesive expression profile in each CLL sample despite the presence of genetic heterogeneity. Our study highlights the potential for single-cell RNA-based targeted analysis to sensitively determine transcriptional and mutational profiles of individual cancer cells leading to increased understanding of driving events in malignancy.</p> <p>Reprinted from Genome Research, with permission from Publisher.</p>
| phs001372 | dbGaP