Ontology highlight
ABSTRACT:
PROVIDER: PRJNA714631 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Ginseng Radix et Rhizoma (GR), Bufonis Venenum (BV), Epimedii Folium (EF), Aconiti Lateralis Radix Praeparata (AL) and Salviae Miltiorrhizae Radix et Rhizoma (SM)
2023-11-27 | MSV000093516 | MassIVE
Project description:To investigate the toxicity of long-term treatment with Asari Radix et Rhizoma on hematopoietic cells, we have performed the 28 days gavage administration of AR in C57BL/6 mouse. Then, we have harvested the RBC lysed bone marrow cells, and analyzed the RNA-seq. analysis.
2022-05-30 | GSE204972 | GEO
Project description:The effect of Asari Radix et Rhizoma on hematopoietic stem cells in C57BL/6 mouse.
| PRJNA842910 | ENA
Project description:Network pharmacology study indicated that Puerarin (PUE), wogonin (WOG), berberine (BER) and glycyrrhetinic acid (GLY) were the active components in GQD and performed synergistic effect on the targets of the Wnt signaling pathway. Pharmacologic research revealed that WOG, BER, GLY performed inhibited effect on SW480 cells and PUE only exhibited effective antitumor activity when combined with GLY. RNA-seq were used to discover synergistic mechanism of PUE-GLY and CTNNB1, CCND1, SMAD4 were identified as synergistic targets inhibited by PUE-GLY. Moreover, mechanism study explored PUE-GLY could affect the Wnt signaling pathway by up-regulated GSK3B and down-regulated CTNNB1 synergistically. Importantly, it showed that GLY could effectively increase the intracellular content of PUE based on HPLC/MS analysis, and this process was achieved by GLY through influencing the targets of membrane’s pathway, such as cell adhesion molecules, focal adhesion and tight junction. Our study revealed multi-target mechanism of GLY, down-regulated CTNNB1 as the material for efficacy and intervene membrane protein (CDH1, CADM1, ITGB2, ICAM1) as courier in the formulae. Moreover, the mechanism of synergistic antitumor action of Puerariae Lobatae Radix (Gegen-Monarch) and Glycyrrhiza Radix et Rhizoma (Gancao-Assistant) on Wnt signaling pathway was explored systematically.
2023-08-12 | GSE157181 | GEO
Project description:This is the validation data for candidate de novo CNV calls made in the asthma trios by Itsara et al., Genome Research 2010. In this study, de novo CNV calls in the asthma data set were initially made with Illumina 550K SNP arrays. Validation was performed with custom Nimblegen array CGH for which DNA was available. de novo CNVs would be expected to validate in the child of each trio tested, and not be detected in either parent. We attempted to validate 9 de novo CNVs in the same number of trios. In 3 cases, paternal DNA was not available leaving a total of 24 distinct samples for hybridization. All samples were hybridized against a previously well-characterized reference (NA15510; see Tuzun et al., Nat Genet 2005).
2010-09-01 | E-GEOD-23572 | biostudies-arrayexpress
Project description:To study the effect of Radix Paeoniae Rubra decoction on tolerance of Staphylococcus aureus.The effect of Radix Paeoniae Rubra on the resistance of Staphylococcus aureus to oxacillin sodium was studied by millipore dilution method in this experiment.At the same time ,conducted on transcriptome analysis of Staphylococcus aureus related genes in Radix Paeoniae Rubra.And to detect the expression level of related genes of Staphylococcus aureus under the action of Radix Paeoniae Rubra by PCR technology.The tolerance of Staphylococcus aureus was decreased obviously when the concentration of Radix Paeoniae Rubra decoction was above 1mg/ml.The effect of Radix Paeoniae Rubra decoction on the expression of tolerance genes femB,pvL and gluM when the concentration of Radix Paeoniae Rubra decoction was above 4mg/ml.When rhe concentration of Radix Paeoniae Rubra is more than 1mg/ml,it can effectively reduce the resistance of Staphylococcus aureus to oxacillin sodium.The reason may be due to the effect of Radix Paeoniae Rubra on the resistance gene of Staphylococcus aureus.
2021-01-30 | GSE165791 | GEO
Project description:We combined multi-omics approaches including de novo transcriptome assembly, ribosome profiling and MS-based peptidomics to study the global role of mRNA translation and small ORFs (sORFs) in rice herbicide resistant mutant.
2021-05-11 | PXD025927 | iProX
Project description:This is the validation data for candidate de novo CNV calls made in the CEU Hapmap by Itsara et al., Genome Research 2010. In this study, de novo CNV calls were initially made with Illumina 1M SNP arrays. Validation of CNV calls was performed with Nimblegen custom array CGH using the extended CEPH pedigrees. A truly de novo CNV would be unobserved in the first generation (CEU trio parents), validated in the second generation (CEU trio children), and assuming no selective effects, transmitted to approximately half of the individuals in the third generation. We attempted validation of 4 de novo CNVs in 3 extended CEPH pedigrees: 1358, 1408, and 1459. 12 samples were hybridized in each of the three pedigrees (36 samples total) against a previously well-characterized reference (GM15510; see Tuzun et al., Nat Genet 2005).
2010-09-01 | E-GEOD-23575 | biostudies-arrayexpress
Project description:This dataset is used for the research work entitled "In-depth analysis of molecular network based on liquid chromatography coupled with tandem mass spectrometry in natural products: importance of redundant nodes discovery". It mainly consists of two parts: Discovery of redundant nodes and Reasons of redundant nodes. The Discovery of redundant nodes section includes MS/MS data of five different natural products with distinct compound structures, namely Ginseng Radix et Rhizoma (GR): GR-neg, Epimedii Folium (EF): EF-neg, Salviae Miltiorrhizae Radix et Rhizoma (SM): SM-neg, Bufonis Venenum (BV): BV-pos, and Aconiti Lateralis Radix Praeparata (AL): AL-pos. The Reasons of redundant nodes section includes MS/MS data of GR and EF at different sample concentrations, as well as BV at different mass spectrometry parameters, such as 1-fold, 2-fold, and 10-fold dilution of GR samples (GR-1x dilution, GR-2x dilution, GR-10x dilution), 1-fold, 2-fold, and 10-fold dilution of EF samples (EF-1x dilution, EF-2x dilution, and EF-10x dilution), BV at different capillary voltages (BV-capillary-1500V-(1-6), BV-capillary-1750V-(1-6), BV-capillary-2000V-(1-6), BV-capillary-2250V-(1-6), and BV-capillary-2500V-(1-6)), BV at different sample cone voltages (BV-SC-10V-(1-6), BV-SC-20V-(1-6), BV-SC-30V-(1-6), BV-SC-40V-(1-6), and BV-SC-50V-(1-6)), and BV at different desolvation temperatures (BV-DT-300-(1-6), BV-DT-400-(1-6), and BV-DT-500-(1-6)).
2024-03-25 | MSV000094404 | MassIVE
Project description:Precise deposition of CpG methylation is critical for mammalian development and tissue homeostasis and is often dysregulated in human diseases. The localization of de novo DNA methyltransferases 3A (DNMT3A) and 3B (DNMT3B) is facilitated by PWWP domain recognition of histone H3 lysine 36 (H3K36) methylation (Baubec et al. 2015, Weinberg et al. 2019) and is normally excluded from CpG islands (CGIs) (Wu et al. 2010). However, CpG methylation of CGIs that are regulated by Polycomb repressive complexes (PRCs) has been observed during embryogenesis (Chen et al. 2019), cellular differentiation (Mohn et al. 2008), and cancer progression (Ohm et al. 2007, Schlesinger et al. 2007, Widschwendter et al. 2007), suggesting that an uncharacterized mechanism exists to compete for de novo DNMT recruitment. Here we report that DNMT3A PWWP domain mutations recently identified in paragangliomas (Remacha et al. 2018) and microcephalic dwarfism (Heyn et al. 2019) promote localization of DNMT3A to CGIs in a PRC1-dependent manner. Genome-wide analysis shows that DNMT3A PWWP mutants redistribute to regions containing ubiquitylation of histone H2A at lysine 119 (H2AK119Ub) deposited by PRC1, irrespective of the levels of PRC2-catalyzed tri-methylation of histone H3 at lysine 27 (H3K27me3). DNMT3A, but not DNMT3B, is capable of directly interacting with H2AK119Ub-modified nucleosomes through a putative amino-terminal ubiquitin-dependent recruitment (UDR) region, which serves as an alternative form of genomic targeting in cells upon loss of PWWP reader function. Ablation of PRC1 abrogates localization of DNMT3A PWWP mutants to CGIs and prevents aberrant hypermethylation at these sites. Our study implies that a balance between DNMT3A recruitment by distinct reader domains guides de novo CpG methylation and may underlie the abnormal DNA methylation landscapes observed in human cancers and developmental disorders.
2021-05-13 | GSE147879 | GEO