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MetabolomicsDirect infusion mass spectrometry metabolomics dataset: a benchmark for data processing and quality control
Direct-infusion mass spectrometry (DIMS) metabolomics is an important approach for characterising molecular responses of organisms to disease, drugs and the environment. Increasingly large-scale metabolomics studies are being conducted, necessitating improvements in both bioanalytical and computatio...
2022-05-16 | MTBLS79 | MetaboLights
MetabolomicsSimultaneously discovering the fate and biochemical effects of pharmaceuticals through untargeted metabolomics
Untargeted metabolomics is an established approach in toxicology for characterising endogenous metabolic responses to xenobiotic exposure. Detecting the xenobiotic and its biotransformation products as part of the metabolomics analysis provides an opportunity to simultaneously gain deep insights int...
2023-07-03 | MTBLS2746 | MetaboLights
MetabolomicsExperimental and computational approaches for deep metabolome annotation with application to the ecotoxicological model organism Daphnia magna

Identifying metabolomes with greater coverage and confidence is a critical step towards interpreting the metabolic basis of human and environmental health. Yet for over two decades the field of metabolomics has been inhibited by limited metabolite identification. To address this, we developed the...

MTBLS2273 | MetaboLights
TranscriptomicsKDM6 Inhibition induces DNA Damage Response (DDR) during ESC Differentiation but not during self-renewal.
The discovery of the first histone demethylase in 2004 (LSD1/KDM1) opened new avenues for the understanding of how histone methylation impacts cellular functions. A great number of histone demethylases have been identified since, which are potentially linked to gene regulation as well as to stem cel...
ORGANISM(S): Mus musculus 
2016-03-11 | E-GEOD-49886 | biostudies-arrayexpress
MetabolomicsInvestigating the Mechanisms of Silver Nanoparticle Toxicity in Daphnia magna: A Multi-Omics Approach
Silver nanoparticles (AgNPs), one of the most common nanomaterials in use today, have been shown to enter the aquatic environment from use of commercially obtained products. Although acute toxicity has been shown in vitro and in vivo, there is still a great deal of uncertainty surrounding the molecu...
2017-05-08 | MTBLS260 | MetaboLights
MetabolomicsMetabolomics reveals an involvement of pantothenate for male production responding to the short-day stimulus in the water flea, Daphnia pulex
Under favorable conditions, the micro-crustacean Daphnia pulex produces female offspring by parthenogenesis, whereas in response to various unfavorable external cues, they produce male offspring to induce sexual reproduction (environmental sex determination: ESD). We recently established a suitable ...
2017-04-03 | MTBLS259 | MetaboLights
TranscriptomicsComparative genomic hybridization of benign epithelial and prostate cancer cell lines derived from the same patient
Copy number alterations in a matched pair of benign epithelial and prostate cancer cell lines derived from the same patient were assessed using array-based comparative genomic hybridisation (aCGH). the cancer cell line showed a gain of chromosome 7, deletion of chromosome 8, gains and losses in chro...
ORGANISM(S): Homo sapiens 
2006-08-04 | E-MEXP-803 | biostudies-arrayexpress
TranscriptomicsEnzymatic methyl-seq of embryonic development in the fat-tailed dunnart (Sminthopsis crassicaudata)
DNA methylation (5mC) is an epigenetic mark that plays a critical role in defining cell fate. Following fertilisation, DNA methylation inherited from gametes must be reprogrammed to establish totipotency and enable the parental-to-zygotic transition. To accomplish this, non-mammalian vertebrates suc...
ORGANISM(S): Sminthopsis crassicaudata 
2025-11-14 | E-MTAB-16076 | biostudies-arrayexpress
GenomicsChIP-seq of H3K27ac in Control and NCoR1 KD CD8α+ DCs at 0hr, 2hr and 6hr of TLR stimulation
H3K27ac ChIP-seq was performed to identify active enhancers in different TLR activated control CD8α+ DCs as well as to understand the role of NCoR1 in regulating TLR specific enhacner activity using H3K27ac ChIP-seq performed in NCoR1 KD DCs. MutuDC1940 cell line were treated with TLR3 ligand poly I...
ORGANISM(S): Mus musculus 
2025-12-03 | E-MTAB-10992 | biostudies-arrayexpress
TranscriptomicsRNAsequencing of WT Huh7 cells and lnc122-/miR-122+ Huh7 cells
to find out the lnc122(precursor of miR-122) role as an independent lncRNA, we designed the lnc122-/miR-122+ Huh7 cells with Lenti-CRISPRi_lnc122 + lenti-CAG-miR-122 combination. lenti-CRISPRi_lnc122 suppresses endogenous lnc122 as well as miR-122 but we add back the miR-122 ectopically.
ORGANISM(S): Homo sapiens 
2026-10-07 | E-MTAB-15726 | biostudies-arrayexpress
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