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MetabolomicsUntargeted metabolomic analysis in cats with naturally occurring inflammatory bowel disease and alimentary small cell lymphoma
Feline chronic enteropathy (CE) is a common gastrointestinal disorder in cats and mainly comprises inflammatory bowel disease (IBD) and small cell lymphoma (SCL). Differentiation between IBD and SCL can be diagnostically challenging. We characterized the fecal metabolome of 14 healthy cats and 22 ca...
2021-07-13 | MTBLS440 | MetaboLights
ModelsAbbott2021 - Prediction of Immunotherapy Response in Melanoma through Combined Modeling of NB and Immune-Related Resistance Mechanisms
In this manuscript, the authors had hypothesized a multi-dimensional approach modeling of both tumor and immune-related molecular mechanisms would better predict immune checkpoint blockade (ICB) response than simpler mutation-focused biomarkers, such as tumor mutational burden (TMB). The authors sho...
2024-07-23 | MODEL2407210001 | BioModels
Machine Learning Model 
MetabolomicsSmall molecule produced by Photorhabdus interferes with ubiquinone biosynthesis in Gram-negative bacteria

We report identification of 3,6-dihydroxy-1,2-benzisoxazole (DHB) in a screen of Photorhabdus and Xenorhabdus, whose symbiotic relationship with eukaryotic nematodes favors secondary metabolites that meet several requirements matching those for clinically useful antibiotics. DHB is produced by Ph...

2024-09-06 | MTBLS10720 | MetaboLights
ProteomicsProteomic profiling of kidney biopsies in nephrotic syndrome
Minimal change disease (MCD) and focal segmental glomerulosclerosis (FSGS) are patterns of kidney injury observed in the filtering units of the kidney known as glomeruli. From the NURTuRE cohort of individuals with nephrotic syndrome (NS), we performed laser microdissection and mass spectrometry ana...
ORGANISM(S): Homo sapiens (Human) 
2024-07-15 | PXD053362 | Pride
Nurture cohort Laser-microdissection Global proteomics Minimal change Focal segmental glomerulosclerosis Nephrotic syndrome 
TranscriptomicsChromosomal translocations are guided by the spatial organization of the genome
The extent to which the three-dimensional organization of the genome contributes to chromosomal translocations is an important question in cancer genomics. We now have generated a high-resolution Hi-C spatial organization map of the G1-arrested mouse pro-B cell genome and mapped translocations from...
ORGANISM(S): Mus musculus 
2012-02-16 | E-GEOD-35519 | biostudies-arrayexpress
ProteomicsThe glomerular circadian clock temporally regulates basement membrane dynamics and podocyte glucocorticoid response
Kidneys were collected from wildtype mice over the course of two circadian cycles (every 4 hours for 48 hours), snap frozen, and later prepared for circadian proteomic analysis The purpose of this study was to investigate the correlation between rhythmic matrix gene expression and matrix protein abu...
ORGANISM(S): Mus musculus (Mouse) 
2026-02-02 | PXD054668 | Pride
Kidney matrix Podocytes Glomerular basement membrane Circadian rhythm Glucocorticoids 
TranscriptomicsExpression evolution in gene groups: Inferring non-neutral regulatory change in pathways from transcriptional profiling data
We profiled the transcriptomes of four Saccharomyces species, as well as pairwise hybrids between three of the species with S. cerevisiae For pairwise comparisons between Saccharomyces cerevisiae and each of S. paradoxus, S. mikatae, and S. bayanus, we performed 3'-end RNA-seq on RNA from each paren...
ORGANISM(S): Saccharomyces cerevisiae x Saccharomyces mikatae 
2013-10-21 | E-GEOD-38875 | biostudies-arrayexpress
MetabolomicsDifferent carboxyl-rich alicyclic molecules proxy compounds select distinct bacterioplankton for oxidation of dissolved organic matter in the mesopelagic Sargasso Sea

Marine dissolved organic matter (DOM) varies in its recalcitrance to rapid microbial degradation. DOM of varying recalcitrance can be exported from the ocean surface to depth by subduction or convective mixing and oxidized over months to decades in deeper seawater. Carboxyl-rich alicyclic molecul...

2024-02-20 | MTBLS3512 | MetaboLights
TranscriptomicsIntegrating Large-Scale Functional Genomic Data to Dissect the Complexity of Yeast Regulatory Networks
A major goal of biology is the construction of networks that predict complex system behavior. We combine multiple types of molecular data, including genotypic, expression, transcription factor binding site (TFBS), and protein-protein interaction (PPI) data previously generated from a number of yeas...
ORGANISM(S): Saccharomyces cerevisiae 
2008-06-15 | E-GEOD-11111 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of fission yeast cell cycle, cdc25 block and release 1
Cell cycle program in fission yeast using the temperature sensitive mutant cdc25-22
ORGANISM(S): Schizosaccharomyces pombe 
2009-01-20 | E-MEXP-57 | biostudies-arrayexpress
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