Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

GNPS - Targeted metabolomics of

ABSTRACT: Compilation of the targeted metabolomics data present in the associated paper: Metabolic mutations induce antibiotic resistance by pathway-specific bottlenecks. See "File names association" table in "supplementary files" to link file names with paper figures.

INSTRUMENT(S): 6495A Triple Quadrupole LC/MS

ORGANISM(S): Escherichia Coli (ncbitaxon:562)

SUBMITTER: Hannes Link

PROVIDER: MSV000094698 | GNPS | Tue May 07 04:15:00 BST 2024

REPOSITORIES: GNPS

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Targeted metabolomics of " Metabolic mutations induce antibiotic resistance by pathway-specific bottlenecks."

Project description:Compilation of the targeted metabolomics data present in the associated paper: Metabolic mutations induce antibiotic resistance by pathway-specific bottlenecks. See "File names association" table in "supplementary files" to link file names with paper figures.

2024-05-07 | MSV000094698 | MassIVE

Untargeted metabolomics of " Metabolic mutations induce antibiotic resistance by pathway-specific bottlenecks."

Project description:Untargeted metabolomics dataset for the paper "Metabolic mutations induce antibiotic resistance by pathway-specific bottlenecks " These are the raw files for metabolites of all 41 isolates in Figure 4b of the paper.

2024-05-07 | MSV000094699 | MassIVE

GNPS - Untargeted metabolomics of

2024-05-07 | MSV000094699 | GNPS

Regulation of Zn and Fe transporters by the GPC1 gene during wheat monocarpic senescence

Project description:TaGPC1 and TaGPC2 are NAC-domain transcription factors which accelerate the onset of senescence and facilitate nutrient translocation in wheat. We developed knockout mutants of these genes in tetraploid wheat and used RNA-seq to identify the effect of these mutations on the wheat flag leaf transcriptome during monocarpic senescence. Several transporter-related genes were identified which were upregulated during senescence and differentially expressed between genotypes. Illumina cDNA libraries were constructed from four biological replicates of three genotypes (WT, gpc-a1 and gpc-a1/gpc-b2) at three timepoints (Heading date, 12 days after anthesis and 22 days after anthesis). Reads were aligned to a collection of assembled genomic contigs from flow-sorted chromosome arms (A and B genomes only) provided by the International Wheat Genome Sequencing Consortium. A custom GTF file was generated to identify 139828 gene loci corresponding to transcribed regions of this reference sequence. Please note that the contig names provided by URGI (http://wheat-urgi.versailles.inra.fr/Seq-Repository) were used in the analysis. Most, but not all, of these loci are present in Ensembl (With a modified name, but the same basic information, chromosome arm and unique contig ID) at ftp://ftp.ensemblgenomes.org/pub/plants/release-22/fasta/triticum_aestivum/dna/ Therefore, the contig IDs from URGI (which are available for all our sequences) were used in the processed data file (i.e. the count table and GFF file) and an additional file describing the corresponding Ensembl names for these was provided (Additional_file_2.xlsx).

2014-12-23 | E-GEOD-60635 | biostudies-arrayexpress

Metabolic mutations induce antibiotic resistance by pathway-specific mechanisms and tolerance by slow-growth

Project description:Metabolic mutations induce antibiotic resistance

| PRJEB75208 | ENA

Multi-omics analysis of BCG macrophage activation

Project description:THP-1-derived macrophages were infected with M. bovis BCG. Separately, proteomic analysis was performed on histones (file names containing IKP) and the total proteome (file names containing JMI).

2024-10-08 | PXD051187 | Pride

Fyn- and Abl-driven interactome and post-translational modifications of DCBLD1 and DCBLD2

Project description:Three related datasets are included, all from immunoprecipitations of FLAG-tagged DCBLD1 and DCBLD2 (human) from 293 cells. Letters at the end of file names denote regions of each gel lave from highest (“A”) to lowest (“B”-X) molecular weight. File names containing “SILAC” are part of a dataset composed of 3 biological replicates (“T1”,”T2”,”T3” in file name) run of 10% or 15% gels (“10” or “15” in file name). DCBLD1 or DCBLD2 were immunoprecipitated from cells alone (light SILAC condition) or with Fyn/Abl (heavy SILAC condition). “Mock”, “Fyn” alone, or “Abl” alone in file names denote control immunoprecipitates, in which the light condition was a mock transfection and the heavy was either a mock or had Fyn/Abl expressed alone. Trypsin was used as the proteolytic enzyme. File names beginning with “Label_free” are part of datasets from LC-MS/MS analysis of DCBLD1 or DCBLD2 immunoprecipitates from 293 lysates. Prior to LC-MS/MS analysis, immunoprecipitates were digested with trypsin and GluC. Only DCBLD1 and DCBLD2 protein bands were analyzed via LC-MS/MS. File names containing “zebrafish” are part of datasets from LC-MS/MS analysis of DCBLD2 immunoprecipitates from 293 extracts that were then incubated with zebrafish extracts. These datasets include tryptic peptides from both human and zebrafish proteins.

2020-08-07 | PXD017723 | Pride

Proteomics data of Escherichia phage vB_EcoS-EE09 isolated from wastewater treatment plant effluent and its infected and non-infected host E. coli DSM613

Project description:This dataset was created to (i) compare the protein expression of E. coli DSM613 cells infected and uninfected with phage vB_EcoS-EE09 and (ii) detect structural proteins of phage vB_EcoS-EE09. Thus, this set provides proteomic data of three setups: 1. Uninfected E. coli DSM613 (file names [file ID]: 04_22A [F40]; 13_ecolicontrol_01 [F13]; 14_ecolicontrol_02 [F14]) 2. E. coli DSM613 infected with phage vB_EcoS-EE09 (file names [file ID]: 02_13A [F39]; 27_ecoliinfected_01 [F27]; 28_ecoliinfected_02 [F28]) 3. Cell-free phage lysate of phage vB_EcoS-EE09 (sample name: 01_EE09)

2023-11-13 | PXD046455 | Pride

Genome wide DNA methylation profiles provide clues to the origin and pathogenesis of germ cell tumors

Project description:Germ cell tumors (GCT) originate from germ cells at different developmental stages (GCT type I – V) They are thought to inherit their methylation profile from (early embryonic) germ cells which undergo a characteristic epigenetic “reset” during maturation. This study aims to provide insight into the developmental timing and underlying biology of the various subtypes of GCTs and their (embryonic) cells of origin by identifying specific and global methylation differences between GCT subtypes. In total, 91 type I-IV GCTs and four cell lines were profiled using the Illumina HumanMethylation450 BeadChip (450K) platform. The data were pre-processed using a validated pipeline and analyzed using an in-house generated extension of the annotation manifest. Marked methylation differences were identified between GCT subtypes both on the global and local level (i.e. differentially methylated regions, imprinting control regions, promoters, etc). GCT subtypes indeed show major similarities to specific stages of (early) developing embryonic germ cells with regard to their methylation profile. The extended annotation manifest for the Illumina 450K platform and methylation datasets are readily available on GEO (GEO accession: GSE58538, GPL18809), providing an integrated hypothesis generating data source for future research. File S1. Differentially methylated regions between tumors classes as discussed in Table 1 of the associated publication. All figures. Please investigate using the genomic position as search term. File S2. Differentially methylated regions between GCT cell lines. DMRforPairs output. Significant results only. Please start from the html file.

2015-02-26 | GSE58538 | GEO

Raw OBE MS data for Stepwise design of pseudosymmetric protein hetero-oligomers

Project description:Online buffer exchange (OBE)-MS data for "Stepwise design of pseudosymmetric protein hetero-oligomers"(https://doi.org/10.1101/2023.04.07.535760). Raw file names correspond to file names given in the reports in Table S7. Data was collected using Xcalibur and data were deconvolved using UniDec (https://github.com/michaelmarty/UniDec)

2023-08-22 | MSV000092722 | MassIVE

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data