Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Large-scale Actinomycete metabolomic dataset UmetaFlow

ABSTRACT: >1000 raw files from actinomycete extracts. ISP2, DNPM, and FPY12 media were used to grow every strain (approximately 100 strains) and triplicates for every treatment. This dataset was used to build and test UmetaFlow, an untargeted metabolomics computational workflow for high-throughput processing and analysis. Not all data were deposited because of confidentiality. Preprint connected to data DOI: 10.26434/chemrxiv-2022-z0t4g

INSTRUMENT(S): Orbitrap ID-X, LC-MS-MS/MS

ORGANISM(S): Actinomyces (ncbitaxon:1654)

SUBMITTER: Karl Tilmann Weber

PROVIDER: MSV000090553 | MassIVE | Wed Oct 19 00:32:00 BST 2022

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

GNPS - Large-scale Actinomycete metabolomic dataset UmetaFlow

Project description:>1000 raw files from actinomycete extracts. ISP2, DNPM, and FPY12 media were used to grow every strain (approximately 100 strains) and triplicates for every treatment. This dataset was used to build and test UmetaFlow, an untargeted metabolomics computational workflow for high-throughput processing and analysis. Not all data were deposited because of confidentiality. Preprint connected to data DOI: 10.26434/chemrxiv-2022-z0t4g

2022-10-19 | MSV000090553 | GNPS

Streptomyces collinus Tu 365 and Kutzneria sp. CA-103260 metabolomics data

Project description:This dataset was used to benchmark UmetaFlow, an untargeted metabolomics workflow for data processing and analysis. Preprint connected to data DOI: 10.26434/chemrxiv-2022-z0t4g

2022-08-01 | MSV000090048 | MassIVE

GNPS - Streptomyces collinus Tu 365 and Kutzneria sp. CA-103260 metabolomics data

2022-08-01 | MSV000090048 | GNPS

GNPS - Commercial standards of Streptomyces antibiotics

Project description:Commercial standards for 8 antibiotics produced by Streptomyces used for method validation for the untargeted metabolomics workflow UmetaFlow (Preprint connected to data DOI: 10.26434/chemrxiv-2022-z0t4g). Compounds: Germicidin A, Germicidin B, Kanamycin, Tetracycline, Thiostreptone, Globomycin, Ampicillin and Apramycin.

2022-08-01 | MSV000090047 | GNPS

An in-cluster Sfp-type phosphopantetheinyl transferase instead of the holo-ACP synthase activates the granaticin biosynthesis under natural physiological conditions

Project description:When cultivated on ISP2 plates for sporulation, the gra-orf32 deletion mutant of Streptomyces vietnamensis produced much more granaticins than in liquid or on solid YEME. The transcriptome analysis showed that the transcription levels of more than 1,600 genes were significantly changed (p < 0.05, log2 fold change >1). Amongst them, 872 genes were upregulated and 762 genes were downregulated on ISP2 plates, compared to those on YEME plates. KEGG pathway enrichment analysis showed that four pathways were enriched significantly, including two type II PKS biosynthesis pathways, namely, the granaticin biosynthetic pathway and the kinamycin-like biosynthetic pathway. These results suggested that the kinamycin-like biosynthetic pathway was activated on ISP2 plates and might associate with the elevated production of granaticins. Most of the PPTase genes kept in low-levels of expression or inactivated, even the expression level of the FAS ACPS gene (SVTN_RS23020) was not as high as expected. Two PPTase genes, SVTN_RS03505 and SVTN_RS28640 were slightly upregulated on ISP2 plate, while the FAS ACPS gene (SVTN_RS23020) was downregulated, compared to those on YEME plates.

2022-12-10 | GSE219231 | GEO

Pyracrimycin A producer-strains

Project description:Data used for the validation of the untargeted metabolomics workflow UmetaFlow (Preprint DOI: 10.26434/chemrxiv-2022-z0t4g) and generated for the publication "Identification of the biosynthetic gene cluster for pyracrimycin A and elucidation of a key reaction during its biosynthesis" by Nielsen J. B. et al. (https://doi.org/10.1021/acschembio.2c00480)

2022-08-01 | MSV000090049 | MassIVE

Polyploidy-associated paramutation in Arabidopsis is determined by small RNAs, temperature, and allele structure

Project description:A role for sRNAs in paramuation is emerging, but their nature and mode of action remain elusive. Paramutation between genetically identical epialleles in Arabidopsis allowed the analysis of associated sRNAs (the data deposited here) and revealed differences connected with gene expression, tissue type, and ploidy.

2020-11-28 | GSE162241 | GEO

Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability

Project description:Cytosine DNA methylation is widely described as a transcriptional repressive mark with the capacity to silence promoters. Epigenome engineering techniques enable direct testing of the effect of induced DNA methylation on endogenous promoters, however, the downstream effects have not yet been comprehensively assessed. Here, we simultaneously induced methylation at thousands of promoters in human cells using an engineered zinc finger-DNMT3A fusion protein, enabling us to test the effect of forced DNA methylation upon transcription, chromatin accessibility, histone modifications, and DNA methylation persistence after the removal of the fusion protein. We find that DNA methylation is often not sufficient to suppress transcription which appears to be driven by the eviction of methyl-sensitive transcriptional repressors. Furthermore, we find that some regulatory networks can override DNA methylation, and that promoter methylation can cause alternative promoter usage. DNA methylation deposited at promoter and distal regulatory regions is rapidly erased after removal of the zinc finger-DNMT3A fusion protein, in a process combining active and passive demethylation. Finally, we demonstrate that induced DNA methylation can exist simultaneously on promoter nucleosomes that possess the active histone modification H3K4me3, or DNA bound by the initiated form of RNA polymerase II. These findings have important implications for epigenome engineering, and demonstrate that the response of promoters to DNA methylation are more complex than previously appreciated.

2022-07-04 | GSE165891 | GEO

A large-scale overexpression screen uncovers two paralogous genes ZCF15 and ZCF26 modulating Candida albicans biofilm gene circuitry (RNA-seq data)

Project description:To identify novel genes modulating Candida albicans biofilm formation, a screen of 2451 overexpression strains allowed us to identify 16 genes whose overexpression significantly reduced biofilm formation. Genome-wide expression and binding analyses were conducted upon overexpression of ZCF15 and ZCF26 and wild type planktonic and biofilm cells were performed. This study has identified new sets of biofilm regulators, including ZCF15 and ZCF26 whose specific role in metabolic remodelling during C. Albicans biofilm development. Triplicates data of RNAseq data are provided here with 6 conditions including the ZCF15 and ZCF16 cases mentioned here above

2022-06-01 | E-MTAB-11383 | biostudies-arrayexpress

NHGRI Large Scale Sequencing Program

Project description:NHGRI Large Scale Sequencing Program

| PRJNA158497 | ENA