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GenomicsThe inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA.
3D-topology of DNA in the cell nucleus provides a level of transcription regulation beyond the sequence of the linear DNA. To study the relationship between transcriptional activity and spatial environment of a gene, we have used allele-specific 4C-technology to produce high-resolution topology maps...
ORGANISM(S): Mus musculus 
2011-06-24 | E-GEOD-29509 | biostudies-arrayexpress
ProteomicsHDX-MS Analysis of Conformation Selection by ATP-competitive Inhibitors and Allosteric Communication in ERK2
Activation of the extracellular signal regulated kinase-2 (ERK2) by phosphorylation has been shown to involve changes in protein dynamics, as determined by hydrogen-deuterium exchange mass spectrometry (HDX-MS) and NMR relaxation dispersion measurements. These can be described by a global exchange b...
ORGANISM(S): Rattus norvegicus (Rat) 
2024-03-20 | PXD048311 | Pride
Atp-competitive inhibition Map kinase Hdx-ms Conformation selection Erk2 
TranscriptomicsShared and unique components of human population structure and genome-wide signals of positive selection in South Asia
To study the population genetic structure and genome-wide signals of positive selection we carried out Illumina genotyping for 142 individuals of Sout Asian origin 142 samples are analysed on thwo different Illumina platforms. 48 of them with Human610-Quad v 1.0 are described herein. 142 samples ar...
ORGANISM(S): Homo sapiens 
2011-12-12 | E-GEOD-33489 | biostudies-arrayexpress
GenomicsOncogene-Mediated Alterations in Chromatin Conformation
Emerging evidence suggests that chromatin adopts a non-random three-dimensional (3D) topology and that the organization of genes into structural hubs and domains affects their transcriptional status. How chromatin conformation changes in diseases such as cancer is poorly understood. Moreover, how on...
ORGANISM(S): Homo sapiens 
2012-05-23 | E-GEOD-37752 | biostudies-arrayexpress
TranscriptomicsGlobal identification of yeast chromosome interactions using genome conformation capture
The objective of this study was to determine the global chromosomal interaction map for exponentially growing Saccharomyces cerevisiae cells using Genome Conformation Capture. Interactions between chromosomes were identified within a population of yeast cells growing exponentially in a semi-defined ...
ORGANISM(S): Saccharomyces cerevisiae 
2009-07-21 | E-GEOD-13648 | biostudies-arrayexpress
TranscriptomicsExtensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection [DGE-seq]
The human genome shares a remarkable amount of genomic sequence with our closest living primate relatives. Researchers have long sought to understand what regions of the genome are responsible for unique species-specific traits. Previous studies have shown that many genes are differentially expresse...
ORGANISM(S): Homo sapiens 
2014-02-13 | E-GEOD-54906 | biostudies-arrayexpress
TranscriptomicsPrimary monocyte to macrophage differentiation involves significant changes in chromosome conformation different from cultured THP-1 cells
Use human native monocyte and induce to macrophae by GM-CSF, reserach the chromatin conformation of these two cell types.
ORGANISM(S): Homo sapiens 
2021-02-23 | E-MTAB-8262 | biostudies-arrayexpress
GenomicsExtensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection [Dnase-seq]
The human genome shares a remarkable amount of genomic sequence with our closest living primate relatives. Researchers have long sought to understand what regions of the genome are responsible for unique species-specific traits. Previous studies have shown that many genes are differentially expresse...
ORGANISM(S): Macaca mulatta 
2014-02-13 | E-GEOD-54907 | biostudies-arrayexpress
ProteomicsModeling flexible protein structure with AlphaFold2 and cross-linking mass spectrometry
We propose a pipeline that combines AlphaFold2 (AF2) and crosslinking mass spectrometry (XL-MS) to model the structure of proteins with multiple conformations. The pipeline consists of two main steps: ensemble generation using AF2, and conformer selection using XL-MS data. For conformer selection, w...
ORGANISM(S): Escherichia coli 
2024-05-24 | PXD046392 | Pride
Crosslinks Monolinks Alphafold2 Idr Flexible protein 
TranscriptomicsMicro-C of Drosophila embryos to investigate chromatin conformation during dorsal-ventral patterning
Micro-C was carried out for control embryos and embryos produced from gd7 mutant mothers. The embryos from mutant mothers produce only a single type along the dorsal-ventral axis (dorsal ectoderm). We used these embryos to compare chromatin conformation across tissues.
ORGANISM(S): Drosophila melanogaster 
2021-01-08 | E-MTAB-9784 | biostudies-arrayexpress
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