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ProteomicsCoordinate Enhancer Reprogramming by GATA3 and AP1 Promotes Phenotypic Plasticity to Achieve Breast Cancer Endocrine Resistance
Phenotypic plasticity has emerged as an important mechanism of therapy resistance in cancers, yet the underlying molecular mechanisms remain unclear. Using an established breast cancer cellular model for endocrine resistance, we show that hormone resistance is associated with enhanced phenotypic pla...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2019-05-24 | MSV000083857 | MassIVE
TranscriptomicsA Genome-Wide Characterization of MicroRNA Genes in Maize
MicroRNAs (miRNAs) are small non-coding RNAs that play essential roles in plant growth and development. We conducted a genome-wide survey of maize miRNA genes, characterizing their structure, expression, and evolution. Computational approaches based on homology and secondary structure modeling ident...
ORGANISM(S): Zea mays 
2009-11-23 | E-GEOD-17943 | biostudies-arrayexpress
ProteomicsMASH Explorer: A Universal Software Environment for Top-Down Proteomics
MASH Explorer, a universal, comprehensive, and user-friendly software environment for top-down proteomics. MASH Explorer integrates multiple spectral deconvolution and database searching algorithms into a single, universal platform which can process top-down proteomics data from various vendor forma...
ORGANISM(S): Homo sapiens (Human) 
2021-09-09 | PXD020615 | Pride
Top-down proteomics  data analysis software  proteoform characterization  intact protein analysis 
TranscriptomicsLigand-Dependent Enhancer Activation Regulated by Topoisomerase-I Activity
The discovery that enhancers are regulated transcription units, encoding eRNAs, has raised new questions about the mechanisms of their activation. Here, we report an unexpected molecular mechanism that underlies ligand-dependent enhancer activation, based on DNA nicking to relieve torsional stress f...
ORGANISM(S): Homo sapiens 
2015-01-22 | E-GEOD-63202 | biostudies-arrayexpress
GenomicsEnhancer-bound LDB1 Regulates a Corticotrope Promoter Pausing Repression Program [ChIP-seq]
Substantial evidence supports the hypothesis that enhancers are critical regulators of cell type determination, orchestrating both positive and negative transcriptional programs; however, the basic mechanisms by which enhancers orchestrate interactions with cognate promoters during activation and re...
ORGANISM(S): Mus musculus 
2015-02-03 | E-GEOD-64483 | biostudies-arrayexpress
TranscriptomicsEnhancer-bound LDB1 Regulates a Corticotrope Promoter Pausing Repression Program [GRO-seq]
Substantial evidence supports the hypothesis that enhancers are critical regulators of cell type determination, orchestrating both positive and negative transcriptional programs; however, the basic mechanisms by which enhancers orchestrate interactions with cognate promoters during activation and re...
ORGANISM(S): Mus musculus 
2015-02-03 | E-GEOD-64515 | biostudies-arrayexpress
ProteomicsSerum Peptidome Profiles Immune Response of COVID-19 Vaccine Administration
The study shows the promise of MALDI-TOF MS-based serum peptidome analysis for the assessment of immune responses activated by COVID-19 vaccination, and discovered a panel of serum peptides biomarkers for COVID-19 vaccination and for NAbs generation. The method developed in this study can help not o...
ORGANISM(S): Homo Sapiens 
2022-08-19 | PXD036159 |
ProteomicsAnalyze the post-translation modification of UVRAG
To explore the role of post-translational modification on UVRAG, we used tandem mass spectrometry (MS/MS) to analyze the UVRAG from cells.
ORGANISM(S): Homo Sapiens 
2022-06-14 | PXD034521 |
ProteomicsATAD2 is a Potential Immunotherapy Target for Patients with Small Cell Lung Cancer Harboring HLA-A*0201
To identify the immune peptides in SCLC tumour cells that can be processed and presented by HLA-I, we performed LC–MS/MS analysis on 11 SCLC cell lines, representing the heterogeneity of SCLC subtypes. Ten of the cell lines were confirmed positive for HLA-I, and one was HLA-I-deficient. To analyse c...
ORGANISM(S): Homo Sapiens 
2024-11-26 | PXD058303 |
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