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GenomicsHigh-throughput pyrosequencing of forum domains termini (FT) isolated and amplified from human HEK293T cells
Forum domains are stretches of chromosomal DNA that are excised from eukaryotic chromosomes during their spontaneous non-random fragmentation. Mostly forum domains are of 50-200 kb in length, although larger domains, up to 500 - 700 kb, are also observed. We performed a genome-wide mapping of forum ...
ORGANISM(S): Homo sapiens 
2013-03-31 | E-GEOD-35065 | biostudies-arrayexpress
GenomicsCTCF demarcates chromatin domains
Insulators are DNA elements, which prevent inappropriate interactions between the neighboring regions of the genome. They can be functionally classified as either enhancer blockers or domain barriers. CTCF (CCCTC binding factor) is the only known major insulator binding protein in the vertebrates a...
ORGANISM(S): Homo sapiens 
2008-10-20 | E-GEOD-12889 | biostudies-arrayexpress
TranscriptomicsHT-SELEX of recombinant C2H2 zinc finger domains of Sall4
To define the sequence preference of SALL4 C2H2 zinc finger domains, we performed SELEX coupled with high-throughput sequencing (HT-SELEX) using the purified SALL4 ZFC1, ZFC2 and ZFC4 domains combined with no protein control experiment.
ORGANISM(S): artificial sequences 
2021-01-05 | E-MTAB-9236 | biostudies-arrayexpress
TranscriptomicsTiling path analysis of Drosophila Schneider 2 cultured cells to map forum domains
Forum domains are stretches of chromosomal DNA that are excised from eukaryotic chromosomes during their spontaneous non-random fragmentation. Mostly forum domains are of 50-200 kb in length, although larger domains, up to 500 - 700 kb, are also observed.

We performed a genome-wide mapping o...
ORGANISM(S): Drosophila melanogaster 
2010-11-01 | E-MEXP-2468 | biostudies-arrayexpress
GenomicsH3K27 modifications define segmental regulatory domains in the Drosophila bithorax complex.
The bithorax complex (BX-C) in the fruit fly, Drosophila melanogaster, is a cluster of homeotic genes that determines the identities the body segments. Expression of these genes is governed by cis-regulatory domains, one for each parasegment, which are arranged on the chromosome in the order of the...
ORGANISM(S): Drosophila melanogaster 
2014-08-14 | E-GEOD-55257 | biostudies-arrayexpress
ProteomicsEngineering human SH2 domains for targeted phospho-proteomics
A comprehensive analysis of the phosphoproteome is essential for understanding molecular mechanisms of human diseases. However, current tools to enrich phosphotyrosine are limited in their applicability and scope. Here, we engineered new superbinder SH2 domains that enrich diverse sets of phosphotyr...
ORGANISM(S): Homo sapiens (Human) 
2023-01-13 | PXD030038 | Pride
Phosphoproteomics Synthetic biology K562 Src homology 2 domains Sh2 superbinders Mass spectrometry Human Structural biology Protein engineering Phosphotyrosine 
GenomicsDomains of genomewide gene expression dysregulation in Down syndrome [RRBS]
Trisomy 21 (T21) is the most frequent genetic cause of cognitive impairment. To assess the perturbations of gene expression in T21, and to eliminate the noise of the genomic variability, we studied the transcriptome of fetal fibroblasts from a pair of monozygotic twins discordant for T21. Here we sh...
ORGANISM(S): Homo sapiens 
2014-04-08 | E-GEOD-55505 | biostudies-arrayexpress
GenomicsRedistribution of the Lamin B1 genomic binding profile affects spatial rearrangement of heterochromatic domains and gene expression during senescence
Senescence is a stress responsive form of stable cell cycle exit. Senescent cells have a distinct gene expression profile, which is often accompanied by the spatial redistribution of heterochromatin into senescence-associated heterochromatic foci (SAHFs). Studying a key component of the nuclear lami...
ORGANISM(S): Homo sapiens 
2013-08-22 | E-GEOD-49341 | biostudies-arrayexpress
GenomicsDomains of genomewide gene expression dysregulation in Down syndrome [Dnase HS mapping]
Trisomy 21 (T21) is the most frequent genetic cause of cognitive impairment. To assess the perturbations of gene expression in T21, and to eliminate the noise of the genomic variability, we studied the transcriptome of fetal fibroblasts from a pair of monozygotic twins discordant for T21. Here we sh...
ORGANISM(S): Homo sapiens 
2014-04-08 | E-GEOD-55425 | biostudies-arrayexpress
TranscriptomicsFunctional analysis of TWIST1 domains regulating smooth muscle cell phenotype
TWIST1, a bHLH transcription factor, regulates mesenchymal specification, differentiation, proliferation and migration during development and in diseases such as cancer. More recently, genome-wide association studies have identified TWIST1 as a causal gene that increases risk for multiple vascular ...
ORGANISM(S): Homo sapiens 
2025-10-14 | E-MTAB-15722 | biostudies-arrayexpress
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