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MetabolomicsData processing, multi-omic pathway mapping, and metabolite activity analysis using XCMS Online

Systems biology is the study of complex living organisms, and as such, analysis on a systems-wide scale involves the collection of information-dense data sets that are representative of an entire phenotype. To uncover dynamic biological mechanisms, bioinformatics tools have become essential to fa...

2017-11-23 | MTBLS572 | MetaboLights
MetabolomicsRA-MAP: mapping the molecular immunological landscape in early rheumatoid arthritis with vaccine controls

Rheumatoid arthritis (RA) is a chronic inflammatory disorder with poorly defined aetiology characterised by synovial inflammation with variable disease severity and drug responsiveness. To investigate the peripheral blood immune cell landscape of RA, we performed comprehensive clinical and molecu...

2021-06-16 | MTBLS1497 | MetaboLights
ProteomicsMASP-II for Mapping the Whole-tissue Spatial Proteome and the Intra-brain Distribution of Monoclonal Antibodies
Spatial proteomics at whole-tissue level provides critical insights into region-specific biological regulations but remains challenging. Previously, we introduced the Micro-scaffold Assisted Spatial Proteomics (MASP) technique, permitting whole-tissue mapping. While promising, this prototype require...
ORGANISM(S): Mus musculus (Mouse) 
2026-08-24 | PXD068767 | Pride
Masp Whole tissue mapping Accurate protein distribution In-depth spatial proteomics Mab intra-brain distribution 
TranscriptomicseQTL mapping in Lake Whitefish Species Pairs.
Mapping of expression quantitative trait loci (eQTL) is a powerful means for elucidating the genetic architecture of gene regulation. Yet, eQTL mapping has not been applied towards investigating the regulation architecture of genes involved in the process of population divergence, ultimately leading...
ORGANISM(S): Coregonus clupeaformis 
2008-09-01 | E-GEOD-11378 | biostudies-arrayexpress
GenomicsPopulation-based whole-genome bisulfite sequencing in multiple human tissues
Analysis of human population methylome variation in adipose tissue and whole blood at single-site resolution by whole genome bisulfite sequencing.
ORGANISM(S): Homo sapiens 
2015-10-26 | E-MTAB-3549 | biostudies-arrayexpress
TranscriptomicsMicroarray-based global mapping of integration sites of retrotransposon, intracisternal A-particle, in mouse genome
Mammalian genomes have evolutionary harbored numerous mobile elements, a part of which are still active and evoke genomic instability. Their movement and positional diversity occasionally result in phenotypic changes and variation by causing altered expression and disruption of neighboring genes in...
ORGANISM(S): Mus musculus 
2008-05-03 | E-GEOD-9572 | biostudies-arrayexpress
TranscriptomicsTranscription profiling and QTL mapping of 60 mice from an F2 sample segregating for diabetes to generate expression trait correlations and expression quantitative trait locus mapping.
Coordinated regulation of gene expression levels across a series of experimental conditions provides valuable information about the functions of correlated transcripts. To map gene regulatory pathways, we used microarray-derived gene expression measurements in 60 individuals of an F2 sample segregat...
ORGANISM(S): Mus musculus 
2008-06-12 | E-GEOD-3330 | biostudies-arrayexpress
GenomicsRapid Genome-Scale Mapping of Chromatin Accessibility in Tissue
Here we introduce a novel technique that specifically identifies Tissue Accessible Chromatin (TACh). The TACh method uses pulverized frozen tissue as starting material and employs one of the two robust endonucleases, Benzonase or Cyansase, which are fully active under a range of stringent conditions...
ORGANISM(S): Mus musculus 
2012-08-10 | E-GEOD-39982 | biostudies-arrayexpress
TranscriptomicsENCODE Transcript Mapping for Total RNA from Human NB4 Cells untreated, treated with RA, and treated with TPA
Transcript Mapping on Affymetrix ENCODE arrays for Total RNA from 4 different samples (2 or 3 technical replicates of each). All of the four same NB4 samples have also been treated with Retanoic Acid (RA) (2 or 3 technical replicates of each). Three of the four same NB4 samples have also been treate...
ORGANISM(S): Homo sapiens 
2010-06-10 | E-GEOD-2679 | biostudies-arrayexpress
TranscriptomicsTissue-specific RNA-seq in human evoked inflammation identifies novel blood and adipose lincRNA signatures of cardio-metabolic diseases
Inappropriate or sustained activation of innate immunity is a pathologic feature of several common cardio-metabolic disorders. Little is known, however, about transcriptomic modulation during inflammatory stress in disease-relevant human tissues. We applied deep RNA sequencing (RNA-seq) during low-d...
ORGANISM(S): Homo sapiens 
2014-01-02 | E-GEOD-50792 | biostudies-arrayexpress
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