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MetabolomicsProtein-metabolite interactomics of carbohydrate metabolism reveal regulation of lactate dehydrogenase

Metabolic networks are interconnected and influence diverse cellular processes. The protein-metabolite interactions that mediate these networks are frequently low affinity and challenging to systematically discover. We developed mass spectrometry integrated with equilibrium dialysis for the disco...

2023-08-07 | MTBLS7237 | MetaboLights
TranscriptomicsSaccharomyces cerevisiae Transcript Isoform mapping
Extensive transcriptional heterogeneity revealed by isoform profiling Application of TIF-Seq (Transcript IsoForm Sequencing) to S.cerevisiae. The method was applied to simultaneously identify the 5' capped mRNA transcription start site and the 3' polyadenylation site in different conditions: WT cell...
ORGANISM(S): Saccharomyces cerevisiae 
2013-05-06 | E-GEOD-39128 | biostudies-arrayexpress
MetabolomicsIntegration of magnetic resonance imaging and protein and metabolite CSF measurements to enable early diagnosis of secondary progressive multiple sclerosis

Molecular networks in neurological diseases are complex. Despite this fact, contemporary biomarkers are in most cases interpreted in isolation, leading to a significant loss of information and power. We present an analytical approach to scrutinize and combine information from biomarkers originati...

2018-08-13 | MTBLS558 | MetaboLights
TranscriptomicsTunable protein synthesis by transcript isoforms in human cells (Transcript Isoforms in Polysomes sequencing: TrIP-seq)
Eukaryotic genes generate multiple mRNA transcript isoforms though alternative transcription, splicing, and polyadenylation. However, the relationship between human transcript diversity and protein production is complex as each isoform can be translated differently. We fractionated a polysome profil...
ORGANISM(S): Homo sapiens 
2016-01-11 | E-GEOD-69352 | biostudies-arrayexpress
TranscriptomicsAlternative Isoform Regulation in Human Tissue Transcriptomes
Through alternative processing of pre-mRNAs, individual mammalian genes often produce multiple mRNA and protein isoforms that may have related, distinct or even opposing functions. Here we report an in-depth analysis of 15 diverse human tissue and cell line transcriptomes based on deep sequencing of...
ORGANISM(S): Homo sapiens 
2008-09-30 | E-GEOD-12946 | biostudies-arrayexpress
MetabolomicsThe novel protein circPETH-147aa regulates metabolic reprogramming in hepatocellular carcinoma cells to remodel immunosuppressive microenvironment
Metabolic reprogramming fuels cancer cell metastasis and remodels the immunosuppressive tumor microenvironment (TME). We report here that a circRNA, circPETH, packaged by extracellular vesicles (EVs) from tumor-associated macrophages (TAMs) to hepatocellular carcinoma (HCC) cells, facilitates glycol...
2024-12-09 | MTBLS11254 | MetaboLights
TranscriptomicsMapping and characterization of promoter-binding sites of protein phosphatase 1
Protein phosphatase 1 (PP1) is a Ser/Thr phosphatase that has been implicated in many key cellular functions including transcriptional regulation. Due to its involvement these many processes, it becomes difficult to directly link PP1 to transcriptional regulation on the chromatin level as no direct ...
ORGANISM(S): Homo sapiens 
2015-06-17 | E-GEOD-54170 | biostudies-arrayexpress
MetabolomicsTargeted metabolomic analysis in hepatic extracts, serum, and urine of female mice gavaged with TCDD every 4 days for 28 days
TCDD is an environmental contaminant that elicits a number of hepatic effects including fat accumulation, inflammation, and fibrosis that can progress to hepatocellular carcinoma. RNA-Seq and targeted metabolomics were integrated with complementary dioxin response element (DRE) location and aryl hyd...
2017-02-02 | MTBLS225 | MetaboLights
TranscriptomicsIdentification of Common Genetic Variants that Account for Transcript Isoform Variation between Human Populations
In addition to the differences between populations in transcriptional and translational regulation of genes, alternative pre-mRNA splicing (AS) is also likely to play an important role in regulating gene expression and generating variation in mRNA and protein isoforms. Recently, the genetic contribu...
ORGANISM(S): Homo sapiens 
2010-08-19 | E-GEOD-9703 | biostudies-arrayexpress
TranscriptomicsIdentification of transcripts regulated by CEBPA protein and its P30 isoform in K562
To investigate the effect of CEBPA and its mutant isoform P30 on the expression of mRNAs and long non-coding RNAs (lncRNAs), we utilized the K562 AML cell line carrying a stable and Tet-on inducible CEBPA or P30 allele. Based on the expression of known CEBPA transcriptional targets, we selected RNA...
ORGANISM(S): Homo sapiens 
2015-06-10 | E-GEOD-65235 | biostudies-arrayexpress
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