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ProteomicsDeep motif deconvolution of HLA-II peptidomes
CD4 T cells are key for priming and regulating immune recognition of infected and cancer cells, but predictions of class II epitopes have limited accuracy. We profiled over 100’000 HLA-II ligands by Mass Spectrometry and developed a novel motif deconvolution algorithm to analyze these data. Our work...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2024-10-18 | MSV000096130 | MassIVE
GenomicsPlasma DNA motif analysis
Plasma DNA motif analysis
EGAS00001003409 | EGA
ModelsCloutier2012 - Feedback motif for Parkinson's disease
Cloutier2012 - Feedback motif for Parkinson's disease This model is described in the article: Feedback motif for the pathogenesis of Parkinson's disease. Cloutier M, Middleton R, Wellstead P. IET Syst Biol 2012 Jun; 6(3): 86-93 Abstract: Previous article on the inte...
2024-09-02 | BIOMD0000000558 | BioModels
ProteomicsMotif-centric phosphoproteomics to target kinase-mediated signaling pathways
Identifying cellular phosphorylation pathways based on kinase-substrate relationships is a critical step to understanding the regulation of physiological functions in cells. Mass spectrometry-based phosphoproteomics workflows have made it possible to comprehensively collect information on individual...
ORGANISM(S): Homo Sapiens (human) 
2021-12-01 | PXD026996 | JPOST Repository
TranscriptomicsTrophoblast-Induced Changes in C-X-C Motif Chemokine 10 Expression Contribute to Vascular Smooth Muscle Cell Dedifferentiation During Spiral Artery Remodeling
Endothelial cell and vascular smooth muscle cell were cocultured in hanging droplets to form spheroids representing an inverted vessel lumen. Control or conditioned media from an extravillous trophoblast (EVT) cell line was incubated with vascular spheroids for 24 hours. Spheroid RNA was then analyz...
ORGANISM(S): Homo sapiens 
2013-02-17 | E-MTAB-1462 | biostudies-arrayexpress
TranscriptomicsAn Extended dsRBD with a Novel Zinc-Binding Motif Mediates Nuclear Retention of Fission Yeast Dicer
Dicer proteins function in RNA interference (RNAi) pathways by generating small RNAs (sRNAs). Here we report the solution structure of the C-terminal domain of Schizosaccharomyces pombe Dicer (Dcr1). The structure reveals an unusual double-stranded RNA binding domain (dsRBD) fold embedding a novel z...
ORGANISM(S): Schizosaccharomyces pombe 
2011-09-22 | E-GEOD-30586 | biostudies-arrayexpress
TranscriptomicsA search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation.
Analysis of the intergenic regions of Staphylococcus aureus by bioinformatics predicted multiple regulatory regions. From this analysis, we also characterized 11 novel noncoding RNAs (RsaA-K) that are expressed in several S. aureus strains under different experimental conditions. Many of them accumu...
ORGANISM(S): Staphylococcus aureus 
2010-05-18 | E-GEOD-17135 | biostudies-arrayexpress
TranscriptomicsBinding motif analysis of METTL3，WTAP in METTL3，WTAP overexpressed Human 293T cells
label the cells overexpressed Myc tagged METTL3 and Flag tagged WTAP with 4-SU, the RNA bound by METT3,WTAP can be got by Myc or Flag IP followed by RNA isolation by using the TRIzol (Invitrogen) reagent by following the company manual.the RNA was then used for library preparation using a TruSeq™ RN...
ORGANISM(S): Homo sapiens 
2014-01-16 | E-GEOD-50580 | biostudies-arrayexpress
Proteomics,MultiomicsProteomics of U1810 cells upon treatment with microRNAs with an AAGUGC seed motif.
microRNA dysregulation is a common feature of cancer cells, but the complex roles of microRNAs in cancer are not fully elucidated. Here we used functional genomics to identify oncogenic microRNAs in non-small cell lung cancer and to evaluate their impact on response to EGFR targeting therapy. Our da...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-31 | MSV000080829 | MassIVE
TranscriptomicsATAC-seq of HEK293 cells with Alu-motif targeted dCas9GFP
HEK293 cells were selected and subcloned for doxycyclin (DOX) and trimethoprim (TMP) inducible dCas9GFP and a guide RNA molecule targeting an EGA enriched Alu-motif (EEA-g1). Cells were treated with DOX and TMP for three days to induce dCas9GFP expression and ATAC-seq samples were collected from tre...
ORGANISM(S): Homo sapiens 
2018-06-07 | E-MTAB-6195 | biostudies-arrayexpress
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