Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

GNPS - Chevrette et al. 2022 Microbiome composition modulates secondary metabolism in a multispecies bacterial community

ABSTRACT: Dataset from Chevrette MG, Thomas CS, Hurley A, Rosario-Melendez N, Sankaran K, Tu Y, Hall A, Magesh S, Handelsman J. Microbiome composition modulates secondary metabolism in a multispecies bacterial community. Proc Natl Acad Sci U S A. 2022 Oct 18;119(42):e2212930119. doi: 10.1073/pnas.2212930119. Epub 2022 Oct 10. PMID: 36215464; PMCID: PMC9586298. Cultures of a simplified model of the rhizosphere, composed of Bacillus cereus (Bc), Flavobacterium johnsoniae (Fj), and Pseudomonas koreensis (Pk). In addition, a Pseudomonas koreensis mutant with the koreenceine BGC deletion (D) was used for cultures. Data were collected using monocultures, as well as two- and three-member cocultures.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Pseudomonas Koreensis (ncbitaxon:198620) Flavobacterium Johnsoniae (ncbitaxon:986) Bacillus Cereus (ncbitaxon:1396)

SUBMITTER: Marc Chevrette Jo Handelsman

PROVIDER: MSV000094118 | GNPS | Mon Feb 19 09:38:00 GMT 2024

REPOSITORIES: GNPS

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Identifying crossover locations in Arabidopsis thaliana h2a.w7 Col-0 × Ler F2 populations using genotyping-by-sequencing

Project description:Genomic DNA from 144 h2a.w7 Col-0 x Ler F2 individuals was extracted using CTAB (as described in Kuo et al, 2022 Methods Mol Biol - PMID: 35461443) and used to generate sequencing libraries as described (Lawrence et al, 2019 Current Biology - PMID: 31378616). Sequencing data was analysed to identify crossovers using the TIGER pipeline as previously described (Rowan et al, 2015 G3 (Bethesda) - PMID: 25585881; Yelina et al, 2015 Genes & Dev - PMID: 26494791; Lawrence et al, 2019 Current Biology - PMID: 31378616).

2025-07-11 | E-MTAB-15040 | biostudies-arrayexpress

Differential gene expression between BGC-823/NC and BGC-823/MTA2, SGC-7901/NC and SGC-7901/shMTA2 cells

Project description:Metastasis associated 1 family, member 2 (MTA2) gene is classified to metastasis associated gene family. We have previously reported that MTA2 gene was overexpressed in gastric cancer tissues, correlating with tumor invasion, lymph node metastasis, and advanced TNM stage. MTA2 knockdown significantly inhibited gastric cancer cell invasion and metastasis. Yet, its molecular mechanisms are still unclear. The aim of this study is to investigate the molecular mechanisms of MTA2 in regulating malignant behaviors of gastric cancer. This experiment captures the expression data between BGC-823/NC and BGC-823/MTA2, SGC-7901/NC and SGC-7901/shMTA2 cells using Whole human genome microarray 4×44K (Design ID: 014850, Agilent technologies).

2015-04-08 | E-MTAB-3469 | biostudies-arrayexpress

Transcription profiling by array of Staphylococcus epidermidis with and without co-culture with Candida albicans

Project description:S. epidermidis cultures vs. cocultures of S. epidermidis and C. albicans (all cultures at 6 hrs of growth)

2011-01-01 | E-MTAB-426 | biostudies-arrayexpress

Acetylated Lysine IP-LC-MS-MS Identifies SirT2 Deacetylation Sites

Project description:The data provided under files section of this file release includes supplemental tables S1 from the publication, Zhang, H., Dammer, E.B., Duong, D.M. et al. Quantitative proteomic analysis of the lysine acetylome reveals diverse SIRT2 substrates. Sci Rep 12, 3822 (2022). https://doi.org/10.1038/s41598-022-06793-5

2025-02-22 | PXD050022 | JPOST Repository

Multiwalled carbon nanotube-induced blood genomic changes following aspiration exposure in mice: A 1-year postexposure study.

Project description:Pulmonary exposure to multiwalled carbon nanotubes (MWCNT) induces an inflammatory and rapid fibrotic response, although the long-term signaling mechanisms are unknown. The aim of this study was to perform genome-wide mRNA profiling in mice blood to identify non-invasive blood based biomarkers for medical and occupational surveillance. The pathological results in this 1-year MWCNT post-exposure study was previously published in Snyder-Talkington et al. J Toxicol Environ Health A. 2016;79(8):352-66. doi: 10.1080/15287394.2016.1159635. Epub 2016 Apr 19. PMID: 27092743

2019-07-26 | GSE126959 | GEO

Paleofuran BGC

Project description:Paleofuran BGC

| PRJEB75212 | ENA

Project description:Accramycin BGC

| PRJNA560219 | ENA

Expression analysis of Plasmodium falciparum 3D7 delta-PfPuf2 mutant

Project description:Investigation of whole genome gene expression level changes in Plasmodium falciparum 3D7 delta-PfPuf2 mutant, compared to the wild-type strain 3D7. The mutation engineered into this strain render tanslational control. The mutants analyzed in this study are further described in Miao J, Li J, Fan Q, Li X, Li X, Cui L.2010. The Puf-family RNA-binding protein PfPuf2 regulates sexual development and sex differentiation in the malaria parasite Plasmodium falciparum. J Cell Sci. 123(7):1039-49 (PMID 20197405). A 12 chip study using total RNA recovered from six separate wild-type cultures of Plasmodium falciparum 3D7 at gametocyte stage III (three cultures) and stage V (three cultures) and six separate cultures of dalta PfPuf2 mutant at gametocyte stage III (three cultures) and stage V (three cultures). Each chip measures the expression level of 5,367 genes from Plasmodium falciparum 3D7 with 45-60 mer probes with two replicates on final array of 71618 probes.

2012-07-05 | E-GEOD-39124 | biostudies-arrayexpress

Expression Analysis of Mammary Epithelial Cells Isolated from 12-16 Week Old Virgin C57Bl6 Lrp5+/+ and Lrp5-/- Mice

Project description:Investigation of whole-genome gene expression level changes in C57Bl6 Lrp5-/- mammary epithelial cells, compared to the wild-type strain. The mammary epithelial cells were isolated from numbers 4 and 5 mammary glands. The Lrp5-/- mouse strain described in this study has been further described in Lindvall C, Evans NC, Zylstra CR, Li Y, Alexander CM, Williams BO. 2006. The Wnt signaling receptor Lrp5 is required for mammary ductal stem cell activity and Wnt1-induced tumorigenesis. J Biol Chem. 2006 Nov 17;281(46):35081-7. Epub 2006 Sep 13. PMID: 16973609.

2009-12-01 | GSE19228 | GEO

Proteomic analysis of nonsmall cell lung cancer

Project description:These data correspond to PMID: 22761400, "In-depth proteomic analysis of nonsmall cell lung cancer to discover molecular targets and candidate biomarkers." (Mol Cell Proteomics. 2012 Oct;11(10):916-32. Epub 2012 Jul 3.)

2013-11-18 | MSV000078491 | 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