Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Addressing batch effects in large-scale metabolomics with augmented experimental design and meta-analysis (Part 1)

ABSTRACT: Non-polar and polar sequential extracts were collected on three groups of C. elegans: natural isolates, central metabolism mutants, and UDP-glucuronosyltrasnferase mutants. Untargeted LC-MS (HILIC/RP - positive and negative mode) and NMR (CDCl3/H2O) studies were conducted using a Vanquish UHPLC coupled to an Orbitrap Elite MS and NEO 800 MHz Bruker NMR spectrometer, respectively. An augmented design, rank transformation of the raw data, strict feature filtering and QA/QC followed by a meta-analysis was performed on all datasets to demonstrate the benefits of this analysis approach and identify stable, significant features to prioritize for downstream compound identification efforts.

ORGANISM(S): Caenorhabditis Elegans C. Elegans

TISSUE(S): Worms

SUBMITTER: Brianna Garcia

PROVIDER: ST002095 | MetabolomicsWorkbench | Tue Feb 22 00:00:00 GMT 2022

REPOSITORIES: MetabolomicsWorkbench

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	mwtab	Other

Items per page:

1 - 1 of 1

Similar Datasets

Addressing batch effects in large-scale metabolomics with augmented experimental design and meta-analysis (Part 2)

Project description:Non-polar and polar sequential extracts were collected on three groups of C. elegans: natural isolates, central metabolism mutants, and UDP-glucuronosyltrasnferase mutants. Untargeted LC-MS (HILIC/RP - positive and negative mode) and NMR (CDCl3/H2O) studies were conducted using a Vanquish UHPLC coupled to an Orbitrap Elite MS and NEO 800 MHz Bruker NMR spectrometer, respectively. An augmented design, rank transformation of the raw data, strict feature filtering and QA/QC followed by a meta-analysis was performed on all datasets to demonstrate the benefits of this analysis approach and identify stable, significant features to prioritize for downstream compound identification efforts.

2022-03-04 | ST002096 | MetabolomicsWorkbench

Addressing batch effects in large-scale metabolomics with augmented experimental design and meta-analysis

Project description:Untargeted LC-MS study conducted using RP and HILIC chromatography on three groups of C. elegans: natural isolates, central metabolism mutants, and UDP-glucuronosyltransferase mutants. An augmented study design, rank transformation of the raw data, strict QA/QC followed by a meta-analysis was used for data analysis.

2022-02-14 | ST002092 | MetabolomicsWorkbench

Project description:VANQUISH

| PRJNA642894 | ENA

Escherichia coli str. K-12 substr. W3110

Project description:Escherichia coli W3110 mutants resistant to LEI-800

| PRJNA855320 | ENA

Expression data from CD4 single positive thymocyte subsets from C57BL/6 mice of 6-8 wks of age

Project description:After positive selection in the thymus, the newly generated single positive (SP) thymocytes are phenotypically and functionally immature and undergo apoptosis upon antigen stimulation. In the thymic medullary microenvironment, SP cells progressively acquire immunocompetence. Negative selection to remove autoreactive T cells also occur at this stage. We have defined four subsets of CD4 SP, namely, SP1, SP2, SP3, and SP4 that follow a functional maturation program and a sequential emergence during mouse ontogeny. We used microarray to detail the global programm of gene expression during the maturation of murine CD4 single positive thymocytes Four subsets of CD4+CD8-CD25-NK1.1- thymocytes from C57BL/6 mice of 6-8 wks of age were purified for RNA extraction and hybridization on Affymetrix microarrays, namely, SP1 (Qa-2-6C10+CD69+), SP2 (Qa-2-6C10-CD69+), SP3 (Qa-2-6C10-CD69-), SP4 (Qa-2+6C10-CD69-).

2012-02-13 | E-GEOD-30083 | biostudies-arrayexpress

Arabidopsis SNAREs SYP121 and SYP122 mediate the secretion of distinct cargo 2 subsets

Project description:SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins drive vesicle fusion and contribute to homoeostasis, pathogen defence, cell expansion, and growth in plants. In Arabidopsis thaliana, the two homologous Qa-SNAREs, SYP121 and SYP122 facilitate the majority of secretory traffic to the plasma membrane. In the absence of stress, the single mutants are indistinguishable from wild-type plants, implying a redundancy in their functions. Nonetheless, several studies suggest differences among the secretory cargo of these SNAREs. To address this issue, we conducted an analysis of the proteins secreted by cultured wild-type, syp121 and syp122 mutant Arabidopsis seedlings. Here, we report that a number of cargo proteins are associated differentially with traffic mediated by SYP121 and SYP122. The data also point to important overlaps between the SNAREs. The findings lead us to conclude that the two Qa-SNAREs mediate distinct, but complementary secretory pathways during vegetative plant growth.

2018-09-18 | PXD009640 | Pride

Global Metabolomics of C. elegans using an augmented reference IROA design

Project description:Global Metabolomics of C. elegans using an augmented reference IROA design

2014-09-13 | ST000100 | MetabolomicsWorkbench

Identification of arsenic trioxide (ATO)-rescuable p53 mutations and temperature-sensitive p53 mutations in p53-null U937 cells using a patient-derived 800 p53 mutation library

Project description:Thousands of diverse p53 mutations have been identified in cancer. The leukemia-treating drug arsenic trioxide (ATO) rescues a part of p53 mutations with high potency. To repurpose ATO in personalized p53-targeted therapy, here we quantitatively determined the frequent 800 p53 mutations, covering 95.8% p53 missense-mutation cases in cancer, for their rescue potencies of cell growth inhibitory activity and mouse tumor suppressive activity by ATO. Furthermore, we determined the temperature sensitivity of 800 mutations in mammalian U937 cells and founded that ATO preferentially rescued temperature-sensitive subtype of structural p53 mutants.

2024-08-01 | GSE182927 | GEO

Treponema vincentii strain:OMZ 800 | isolate:OMZ 800

Project description:Treponema vincentii strain:OMZ 800 | isolate:OMZ 800 Genome sequencing

| PRJNA1164405 | ENA

Naked mole rat cells show resistance to iPSC reprogramming and signs of more stable epigenome

Project description:Naked mole rat (NMR) is a valuable model for aging and cancer research due to its exceptional longevity and resistance to tumorigenesis. In an effort to generate NMR induced pluripotent stem cells (iPSCs) we observed that reprogramming efficiency of NMR fibroblasts in repsonse to OSKM overexpression was drasticaly lower than that of mouse fibroblasts. To understand the cause of NMR resistance to reprogramming we screened for factors that improve reprogramming effciency. We identified that expression of SV40 Large T (LT) dramatically improved reprogramming of NMR fibroblasts. Inactivation of Rb alone, but not p53, was suffcient to improve reprogramming effciency suggesting that NMR chromatin structure is refractory to reprogramming. Analysis of global histone landscape using quantitative mass spectrometry revealed that NMR fibroblasts had higer levels of repressive H3K27 methylation marks, and lower levels of activating H3K27 acetylation mark than the mouse fibroblasts. Furthermore, the NMR cells had lower levels of permissive H2A.Z acetylation marks. ChIP showed that of E-cadherin had repressive H3K9me3 histone mark in the NMR, but was poised with a bivalent H3K4me3/H3K27me3 in the mouse. Expression of LT reduced the levels of H3K9me3 mark on E-cadherin promoter. ATAC-seq revealed that NMR had more open chromatin globally, however, NMR promoters were more closed than mouse promoters. Expression of LT antigen led to massive opening of the NMR promoters including gene promoters required for reprogramming. Cumulatively, these data suggest that NMR has more stable epigenome than mouse, which resists reprogramming and may contribute to NMR longevity and cancer resistance.

2017-06-21 | GSE83585 | GEO

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