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ProteomicsAffinity peptide ligands: New tools for chasing non-canonical N-phosphoproteome
Protein N-phosphorylation enrichment is faced with great difficulties due to the intrinsic instability of the N-P bond, which has seriously hindered its biological function unraveling. Current methods for N-phosphopeptides enrichment are challenging to fulfil high selectivity for all types of N-phos...
ORGANISM(S): Homo Sapiens Escherichia Coli Mus Musculus 
2024-12-12 | PXD058797 |
GenomicsProtein/DNA in vitro Binding seq (PB-seq) for Drosophila HSF and genomic Drosophila DNA
DNA sequence and local chromatin landscape act jointly to determine transcription factor (TF) binding intensity profiles. To disentangle these influences, we developed an experimental approach, called protein/DNA binding and high-throughput sequencing (PB-seq), that allows the binding energy landsca...
ORGANISM(S): Drosophila melanogaster 
2012-02-06 | E-GEOD-32570 | biostudies-arrayexpress
ProteomicsMapping the peptide binding groove of MHC class I
An essential element of adaptive immunity is the selective binding of peptide antigens by major histocompatibility complex (MHC) class I proteins and their presentation to cytotoxic T lymphocytes on the cell surface. Using native mass spectrometry, we here analyze the binding of peptides to an empty...
ORGANISM(S): Homo sapiens (Human) 
2022-05-31 | PXD027725 | Pride
Peptide-binding Hla-a Native ms Human Mhc class i 
TranscriptomicsChromosomal High Affinity Binding Sites for the Drosophila Dosage Compensation Complex.
We identified 131 high affinity sites of the Drosophila DCC combining residual ChIP-chip profiles after differential crosslinking and RNAi-mediated knockdown of spreading factors Keywords: ChIP-chip MSL1 and MSL2 ChIP under various conditions including differential crosslinking and RNAi against MOF...
ORGANISM(S): Drosophila melanogaster 
2008-12-13 | E-GEOD-12292 | biostudies-arrayexpress
ProteomicsBiosynthesis and secretion of the microbial sulfated peptide RaxX and binding to the rice XA21 immune receptor
The rice immune receptor XA21 is activated by the sulfated microbial peptide RaxX (required for activation of XA21-mediated immunity X) produced by Xanthomonas oryzae pv. oryzae (Xoo). Mutational studies and targeted proteomics revealed that RaxX is processed and secreted by the protease/transporter...
ORGANISM(S): Xanthomonas Oryzae Pv. Oryzae 
PXD013389 | panorama
GenomicsIdentification of Host-Chromosome Binding Sites and Candidate Gene Targets for KSHV LANA
LANA is essential for tethering the KSHV genome to metaphase chromosomes and for modulating host-cell gene expression, but the binding sites in the host-chromosome remain unknown. Here, we use LANA-specific chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) to identify ...
ORGANISM(S): Homo sapiens 
2012-01-06 | E-GEOD-34890 | biostudies-arrayexpress
TranscriptomicsSingle-cell RNA sequencing of OT-I CD8+ T cells after stimulation with different affinity ligands
Activation of CD8+ T cells depends exquisitely on the affinity of the T cell receptor (TCR) for a peptide MHC (pMHC) ligand complex. Here, we activated OT-I transgenic CD8+ T cells with pure peptide and examined early activation responses by single-cell RNA-sequencing. T cells were activated with th...
ORGANISM(S): Mus musculus 
2018-06-25 | E-MTAB-6051 | biostudies-arrayexpress
UnknownControlling Affinity Binding with Peptide-Functionalized Poly(ethylene glycol) Hydrogels.
Not available
S-EPMC2818180 | biostudies-literature
TranscriptomicsRNA-affinity isolations 13 RBPs
To identify RNAs specifically associated with potential RBPs, yeast cells expressing TAP-tagged RBP or the wild-type strain BY4741 (mock control) were grown to mid-log phase in rich medium and harvested by centrifugation. RNA affinity isolations were essentially performed as described (Gerber et al...
ORGANISM(S): Saccharomyces cerevisiae 
2010-12-06 | E-GEOD-21864 | biostudies-arrayexpress
UnknownQuantification of Uncertainty in Peptide-MHC Binding Prediction Improves High-Affinity Peptide Selection for Therapeutic Design.
Not available
S-EPMC6715517 | biostudies-literature
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