Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

TMT-10plex-based phosphoproteomics of bioactive compounds in A549 cells

ABSTRACT: We conducted a comprehensive screening of bioactive compounds sourced from natural products, specifically targeting those capable of inducing apoptosis while inhibiting tyrosine kinase activity. Our investigation encompassed a diverse range of compounds, including pure compounds, compound mixtures, and peptides, all evaluated within the A549 cell line. To delve into the underlying molecular mechanisms, we employed phosphoproteomics analysis, which enabled us to comprehensively assess the impact of these bioactive compounds on cellular pathways. Through labeling digested proteins with distinct isobaric tags, we meticulously examined the cellular response to each compound. In our experimental design, we included two established chemical drugs, Afatinib and Osimertinib, serving as positive controls. These drugs, both kinase inhibitors utilized in cancer treatment, operate via distinct mechanisms and target different kinases. By comparing the effects of our test compounds with these controls, we aimed to elucidate their potential therapeutic relevance and mechanisms of action. Among the compounds examined were extracts from Phallus indusiatus and Fomes rimosus (Berk.) Cooke, as well as specific compounds like Chamuangone, Cannabigerol (CBG), Cannabidiol (CBD), and NP1-cyclic peptide

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Cell Culture

SUBMITTER: Sucheewin Krobthong

LAB HEAD: Sucheewin Krobthong

PROVIDER: PXD050555 | Pride | 2024-03-13

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	A549_phosphoproteomics_final.xlsx	Xlsx
	T10_01.raw	Raw
	T10_02.raw	Raw
	T10_03.raw	Raw
	T15_01.raw	Raw

Items per page:

1 - 5 of 14

Similar Datasets

Exploring the effect of citronellol on Candida albicans using proteomics appraoch

Project description:To explore the proteome profiles of Candida albicans exposed to citronellol. We used label-free proteomics approach.

2022-05-04 | PXD030379 | Pride

Streptomyces sp. CS7

Project description:Bioprospecting bioactive compounds from Streptomyces sp.

| PRJNA792017 | ENA

Utilizing of quantitative proteomics to identify species-specific protein therapeutic target for treatment of leishmaniasis.

Project description:Identification of common Leishmania antigen proteins is important for practical purposes ranging from diagnostic to the development of a vaccine for the prevention of leishmaniasis. Moreover, we need to establish the potential drug targets that interrupt the replication and transmission of the pathogen to promote drug discovery. Therefore, the objective of this work was to provide the public proteome database which would be useful for the establishment of novel protein antigenicity for therapeutic purposes. This information would introduce the alternative protein targets for Leishmaniasis, allowing the development of therapeutic strategies for the disease.

2022-05-20 | PXD026304 | Pride

Bioactive Compounds from Endophytic fungus Curvularia sorghina

Project description:Bioactive Compounds from Endophytic fungus Curvularia sorghina

| PRJEB25627 | ENA

LC-MSMS of media agar from co-cultivation of Auricularia cornea and Pseudonocardia mangrovi

Project description:The co-cultivation investigation showed that A. cornea TBRC 12900 co-cultivated with P. mangrovi TBRC-BCC 42794 showed a high level of A. cornea mycelial growth. Proteomics analysis was employed to reveal predicted biological activities involved in the mutualistic relationship between the two strains during mycelial growth.

2022-10-27 | PXD035814 | Pride

Serum proteomics analysis of CCA

Project description:Differential plasma proteomes of the patients with Opisthorchiasis viverrini and cholangiocarcinoma identifies polymeric immunoglobulin receptor as potential biomarker

2023-03-10 | PXD028152 | Pride

Expression data from LPS-stimulated RAW 264.7 mouse macrophages treated with Hypericum perforatum fraction and bioactive constituents

Project description:Hypericum perforatum extracts have been used as dietary supplements to treat conditions including mild-moderate depression and inflammation. A group of four bioactive constituents were identified from an active fraction of the extract. In order to identify the mechanism for the potential anti-inflammatory activity of the identified compounds, we used Affymatrix microarray to study the gene expression profile impacteded by these compounds, as well as the active fraction in LPS-stimulated mouse macrophages. We treated RAW264.7 mouse macrophages with DMSO control, active fraction from Hypericum perforaum extract, and a combination of the 4 putative bioactive compounds, called the 4-component system, all with and without LPS induction. A total of six treatment combinations were included in the final gene expression analysis using microarray.

2010-05-28 | E-GEOD-21841 | biostudies-arrayexpress

Effect of LINC00899 depletion on histone mark enrichment in HeLa cells

Project description:LncRNAs represent a major transcriptional output of the human genome, but the function of many of these elements is unknown. In this experiment, we have used the ‘CUT&RUN’ technique to quantify the changes in histone mark enrichment across the genome upon depletion of the lncRNA LINC00899 in HeLa cells. LINC00899 is of interest as its depletion results in mitotic delay, suggesting a role in mitotic progression. The CUT&RUN procedure uses antibodies to target a nuclease to the relevant protein binding site, cleaving the surrounding DNA for sequencing and yielding output equivalent to that of ChIP-seq. This experiment contains 2 replicate batches where each batch contains a sample with LINC00899 knocked down by RNA interference (RNAi); a RNAi negative control; a sample with LINC00899 knocked down with locked nucleic acid antisense oligonucleotides (LNA); and a LNA negative control. This was performed using antibodies against H3K4me3, H3K27ac, H3K36me3 and H3K27me3, as well as an IgG (goat-derived anti-rabbit) control. All samples in each batch were generated at the same time. Within each batch, all CUT&RUN experiments with the same knockdown were performed on nuclei obtained from the same cell culture. Independent cell cultures were used for experiments with different knockdown or in different batches.

2019-03-29 | E-MTAB-7419 | biostudies-arrayexpress

Sensitive mapping of chromatin-altering polymorphisms reveals molecular drivers of autoimmune disease

Project description:Although most disease associations detected by GWAS are nongenic, very few have been mapped to causal regulatory variants. Here, we present a method for detecting regulatory QTLs that does not require genotyping or whole-genome sequencing. The method combines deep, long-read ChIP-seq with a new statistical test that simultaneously scores peak height correlation and allelic imbalance: the Genotype-independent Signal Correlation and Imbalance (G-SCI) test. We performed histone acetylation ChIP-seq on 57 human lymphoblastoid cell lines and used the resulting reads to call 500,066 SNPs de novo within regulatory elements. The G-SCI test annotated 8,764 of these as histone acetylation QTLs (haQTLs) - an order of magnitude larger than the set of candidates detected by expression QTL analysis. Lymphoblastoid haQTLs were highly predictive of autoimmune disease mechanisms. Thus, our method facilitates large-scale regulatory variant detection in any moderately-sized cohort for which functional profiling data can be generated, thus simplifying identification of causal variants within GWAS loci. We applied our method, named Regulatory Variant Ascertainment and chromatin Regression by sequencing (RegVAR-seq), to 57 cell lines from a single population group. We used the resulting sequence data for variant calling, and validated calls using an independent platform. We then identified histone acetylation QTLs (haQTLs) using a novel statistical test that requires no prior genotype information and combines peak height and allelic imbalance data across the 57 individuals. Transcription factor binding site analysis was used to independently support the functionality of haQTLs. Finally, we examined the association between haQTLs and SNPs associated with human phenotypes.

2015-03-01 | E-GEOD-58852 | biostudies-arrayexpress

ZFP462 safeguards neural lineage specification by targeting G9A/GLP-mediated heterochromatin to silence enhancers

Project description:ZNF462 haploinsufficiency is linked to Weiss-Kruszka Syndrome, a genetic disorder characterized by neurodevelopmental defects including Autism. Though conserved in vertebrates and essential for embryonic development the molecular functions of ZNF462 remain unclear. We identified its murine homolog ZFP462 in a screen for mediators of epigenetic gene silencing. Here, we show that ZFP462 safeguards neural lineage specification of mouse embryonic stem cells (ESCs) by targeting the H3K9-specific histone methyltransferase complex G9A/GLP to silence mesoendodermal genes. ZFP462 binds to transposable elements (TEs) that are potential enhancers harboring ESC-specific transcription factor (TF) binding sites. Recruiting G9A/GLP, ZFP462 seeds heterochromatin, restricting TF binding. Loss of ZFP462 in ESCs results in increased chromatin accessibility at target sites and ectopic expression of mesoendodermal genes. Taken together, ZFP462 confers lineage- and locus-specificity to the broadly expressed epigenetic regulator G9A/GLP. Our results suggest that aberrant activation of lineage non-specific genes in the neuronal lineage underlies ZNF462-associated neurodevelopmental pathology.

2023-05-10 | PXD037238 | Pride