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TranscriptomicsWhole-genome Haplotype Reconstruction using Proximity-ligation and Shotgun Sequencing
Rapid advances in high-throughput DNA sequencing technologies are accelerating the pace of research into personalized medicine. While methods for variant discovery and genotyping from whole genome sequencing (WGS) datasets have been well established, linking variants together into a single haplotype...
ORGANISM(S): Homo sapiens 
2013-11-03 | E-GEOD-48592 | biostudies-arrayexpress
TranscriptomicsIn vivo proximity labeling and sequencing (IPL-seq) for SNRPN70 in 293T-Rex
This proof-of-principle experiment was designed to demonstrate the feasibility of proximity labeling for RNAM-bM-^@M-^Sprotein interactions IPL-seq on 293T-Rex expressing MSA-SNRPN70 (sample) or NFH-SNRPN70 (control)
ORGANISM(S): Homo sapiens 
2014-10-24 | E-GEOD-55370 | biostudies-arrayexpress
ProteomicsMapping glycan-mediated galectin-3 interactions by live cell proximity labeling
Galectin-3 is a glycan-binding protein (GBP) that binds β -galactoside glycan structures to orchestrate a variety of important biological events, including the activation of hepatic stellate cells and regulating immunological responses. While the requisite glycan epitopes needed to bind galectin-3 h...
ORGANISM(S): Homo sapiens (Human) 
2021-06-16 | PXD021622 | Pride
Proteomics Galectins Proximity labeling 
TranscriptomicsChromosome positioning and the clustering of functionally related loci in yeast is driven by chromosomal interactions
In recent years there has been considerable and growing interest in the 3-dimensional organization of genomes. In yeast this has included detailed FISH studies that show a surprising degree of spatial clustering of the tRNA genes, the localization of telomeres, centromere positioning, and global stu...
ORGANISM(S): Saccharomyces cerevisiae 
2012-07-18 | E-GEOD-33018 | biostudies-arrayexpress
GenomicsComputational frameworks for predicting protein interactions via single-cell proximity sequencing
Computational frameworks for predicting protein interactions via single-cell proximity sequencing
PRJNA803449 | ENA
ProteomicsProximity labelling and SILAC based proteomic approach identifies proteins at the interface of homotypic and heterotypic cancer cell interactions.
Cell-cell interactions are critical for the growth of organisms and maintaining homeostasis. In the tumor microenvironment, these interactions promote cancer progression. Given their importance in healthy and diseased conditions, we have developed a method to analyze the cell-to-cell interactome. Ou...
ORGANISM(S): Homo sapiens (Human) 
2025-05-26 | PXD052746 | Pride
Silac based Orbitrap Hrp Cell-cell interactions 
ProteomicsProximity labelling and SILAC based proteomic approach identifies proteins at the interface of homotypic and heterotypic cancer cell interactions.
Cell-cell interactions are critical for the growth of organisms and maintaining homeostasis. In the tumor microenvironment, these interactions promote cancer progression. Given their importance in healthy and diseased conditions, we have developed a method to analyze the cell-to-cell interactome. Ou...
ORGANISM(S): Homo sapiens (Human) 
2025-05-26 | PXD060134 | Pride
Silac based  proteomics Nano lc-ms/ms orbitap Cell-cell interactions 
ProteomicsProximity labelling and SILAC based proteomic approach identifies proteins at the interface of homotypic and heterotypic cancer cell interactions.
Cell-cell interactions are critical for the growth of organisms and maintaining homeostasis. In the tumor microenvironment, these interactions promote cancer progression. Given their importance in healthy and diseased conditions, we have developed a method to analyze the cell-to-cell interactome. Ou...
ORGANISM(S): Homo sapiens (Human) 
2025-05-26 | PXD052917 | Pride
Silac based  proteomics Nano lc-ms/ms orbitap Cell-cell interactions 
GenomicsComprehensive mapping of long-range interactions reveals folding principles of the human genome.
We describe Hi-C, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. We constructed spatial proximity maps of the human genome with Hi-C at a resolution of 1Mb. These maps confirm the presence of chromosom...
ORGANISM(S): Homo sapiens 
2009-10-09 | E-GEOD-18199 | biostudies-arrayexpress
TranscriptomicsInteractions among Polycomb domains are guided by chromosome architecture
Polycomb group (PcG) proteins bind and regulate hundreds of genes. Previous evidence has suggested that long-range chromatin interactions may contribute to the regulation of PcG target genes. Here, we adapted the Chromosome Conformation Capture on Chip (4C) assay to systematically map chromosomal in...
ORGANISM(S): Drosophila melanogaster 
2011-05-09 | E-GEOD-23166 | biostudies-arrayexpress
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