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MetabolomicsComprehensive lipid analysis of green Arabica coffee beans by LC-HRMS/MS
Lipids play an important role in coffee bean development, coffee brew and in the effects of coffee on human health. They account for around 17% of the dry bean weight and encompass different classes and subclasses, mostly triacylglycerols (TAG) and a minor quantity of phospholipids (PL) and βN-alkan...
2021-11-19 | MTBLS1972 | MetaboLights
ProteomicsSelective targeting of TBXT with DARPins identifies regulatory networks and therapeutic vulnerabilities in chordoma
Aberrant expression of the embryonal transcription factor TBXT (also known as brachyury) drives chordoma, a rare spinal neoplasm with no effective drug therapies. The gene network regulated by TBXT is poorly understood, and strategies to disrupt its abnormal activity for therapeutic purposes are lac...
ORGANISM(S): Homo sapiens (Human) 
2025-07-31 | PXD055982 | Pride
Tbxt Chordoma Darpin Brachyury 
MetabolomicsObesogenic high-fat diet and MYC cooperate to promote lactate accumulation and tumor microenvironment remodeling in prostate cancer (Murine serum assays)

Cancer cells exhibit metabolic plasticity to meet oncogene-driven dependencies while coping with nutrient availability. A better understanding of how systemic metabolism impacts the accumulation of metabolites that reprogram the tumor microenvironment and drive cancer could facilitate development...

2024-04-10 | MTBLS3316 | MetaboLights
MetabolomicsObesogenic high-fat diet and MYC cooperate to promote lactate accumulation and tumor microenvironment remodeling in prostate cancer (Murine prostate assays)

Cancer cells exhibit metabolic plasticity to meet oncogene-driven dependencies while coping with nutrient availability. A better understanding of how systemic metabolism impacts the accumulation of metabolites that reprogram the tumor microenvironment and drive cancer could facilitate development...

2024-04-10 | MTBLS3317 | MetaboLights
TranscriptomicsRNA Affinity Purification followed by sequencing (RAP-seq) allows identification of transcriptome-wide RBP binding sites using recombinant RBPs and purified total cellular RNA
RAPseq is a new in vitro method used to study RNA-protein interactions at scale. In RAPseq, a recombinant RBP is produced as fusion with a HaloTag which is used to recover and purify the RBP of interest. The RBP-Halo fusion is then incubated with fragmented native total RNA that retains endogenous s...
ORGANISM(S): Homo sapiens 
2023-12-29 | E-MTAB-10834 | biostudies-arrayexpress
TranscriptomicsComparative gene expression in floral whorls of the basal eu-dicot Aquilegia formosa
Investigation of genome-wide gene expression in sepals, petals, stamens, staminodia and carpels in pre-anthesis Aquilegia flowers. One goal was to identify transcriptional signatures associated with petaloidy by comparing gene expression in petals and petaloid sepals. Other goals were to study the e...
ORGANISM(S): Aquilegia formosa 
2010-05-18 | E-GEOD-19432 | biostudies-arrayexpress
TranscriptomicsChromatin modifications induced by PML-RARalpha repress critical targets in leukemogenesis as analyzed by ChIP-Chip.
A global view of PML-RAR? transcriptional functions was obtained by genome-wide binding and chromatin modification analyses, combined with genome wide expression data. Complete Abstract: The translocation t(15;17) generates the chimeric PML-RAR? transcription factor that is the initiating event of ...
ORGANISM(S): Homo sapiens 
2008-09-06 | E-GEOD-12641 | biostudies-arrayexpress
TranscriptomicsWhole blood expression profiling from a general population (KORA F4)
The development of whole genome association studies from the general population has lead to the robust identification of several loci involved in different common human diseases. Interestingly, most of the strongest signals of association observed in these studies arise from non-coding regions, rais...
ORGANISM(S): Homo sapiens 
2013-07-13 | E-MTAB-1708 | biostudies-arrayexpress
TranscriptomicsRicochet transcription of pachytene piRNA promoters in mammals
The origin and stability of germline noncoding RNAs remain largely uncharacterized in mammals. Here, we demonstrate that the vast majority of pachytene piRNAs originate from less than 100 bi- and unidirectionally transcribed loci in the mouse genome. These loci show features characteristic of trans...
ORGANISM(S): Mus musculus 
2015-09-01 | E-MTAB-1265 | biostudies-arrayexpress
TranscriptomicsExpression analysis of Vibrio cholerae O395N1 delta-nqrA-F mutant
Investigation of whole genome gene expression level changes in a Vibrio cholerae O395N1 delta-nqrA-F mutant, compared to the wild-type strain. Total RNA recovered from wild-type cultures of VIbrio cholerae O395N1 and its nqrA-F mutant strain. Each chip measures the expression level of 3,835 genes f...
ORGANISM(S): Vibrio cholerae 
2014-04-01 | E-GEOD-56387 | biostudies-arrayexpress
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