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GenomicsDNA sequence quantitatively encodes CTCF-binding affinity at genome scale
DNA sequence quantitatively encodes CTCF-binding affinity at genome scale
PRJNA1194604 | ENA
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
ProteomicsCharacterizations of HSP90-interacting complex in renal cells using tandem affinity purification and its potential role in kidney stone formation
Heat shock protein 90 (HSP90) is a highly abundant molecular chaperone that interacts with many other intracellular proteins to regulate various cellular processes. However, compositions of the HSP90-interacting complex remain underinvestigated. This study thus aimed to characterize such complex in ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2018-12-17 | MSV000083252 | MassIVE
GenomicsLow affinity CTCF binding drives transcriptional regulation whereas high affinity binding encompasses architectural functions.
Low affinity CTCF binding drives transcriptional regulation whereas high affinity binding encompasses architectural functions.
PRJNA856492 | ENA
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
GenomicsHigh-resolution mapping of transcription factor binding sites on native chromatin
Sequence-specific DNA-binding proteins including transcription factors (TFs) are key determinants of gene regulation and chromatin architecture. Formaldehyde cross-linking and sonication followed by Chromatin ImmunoPrecipitation (X-ChIP) and sequencing is widely used for genome-wide profiling of pro...
ORGANISM(S): Drosophila melanogaster 
2013-12-14 | E-GEOD-45672 | biostudies-arrayexpress
GenomicsCBFβ-SMMHC-driven leukemogenesis requires enhanced RUNX1-DNA binding affinity in mice
CBFβ-SMMHC-driven leukemogenesis requires enhanced RUNX1-DNA binding affinity in mice
PRJNA1206157 | ENA
TranscriptomicsQuantitative modeling of transcription factor binding specificities using DNA shape
Accurate predictions of the DNA binding specificities of transcription factors (TFs) are necessary for understanding gene regulatory mechanisms. Traditionally, predictive models are built based on nucleotide sequence features. Here, we employed three- dimensional DNA shape information obtained on a ...
ORGANISM(S): Homo sapiens 
2014-11-04 | E-GEOD-59845 | biostudies-arrayexpress
ProteomicsIdentification of inositol 1,4,5-trisphosphate-binding proteins by heparin-agarose affinity purification and LTQ ORBITRAP MS in Oryza sativa
Inositol 1,4,5-trisphosohate (IP3) and its receptors play a pivotal role in calcium signal transduction in mammals. Some fractions of tonoplast and endoplasmic reticulum membranes have high affinity binding activity for IP3, and IP3 can induce Ca2+ release in several plants. However, no homologues o...
ORGANISM(S): Oryza sativa (Rice) 
2014-09-25 | PXD000763 | Pride
Oryza sativa Ip3 Ip3 binding protein Ltq orbitrap ms Heparin-agarose 
ProteomicsMS for RNA binding preteins in tapasin 3'UTR
Using affinity purification for the detection of RNA-binding proteins in tapasin 3'UTR
ORGANISM(S): Homo sapiens (Human) 
2025-05-06 | PXD045056 | Pride
Tapasin 3'utr 
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