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ProteomicsSingle-copy locus isolation identifies distinct proteomes of early- and late-firing DNA replication origin chromatin
The chromatin at origins of replication is the template for DNA replication initiation in eukaryotic genomes. However, whether the chromatin composition instructs individual origins to fire early-efficiently (EE) or late-inefficiently (LI) remains to be investigated. Here, we used site-specific reco...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2023-05-10 | PXD031984 | Pride
Replication timing Replication efficiency Affinity purification Locus-specific chromatin isolation Dna replication origin Histone ptms Site-specific recombination 
ProteomicsMudPIT analyses of the proteins purified by in vitro dCas9-targeted chromatin IP of the fruit fly Histone Cluster
We used a reverse chromatin immunoprecipitation (ChIP) method that takes advantage of the RNA-mediated DNA-targeting capability of Cas9 to efficiently and adaptably isolate specific genomic regions and their associated protein factors. By using purified recombinant catalytically-dead Cas9 (dCas9) co...
ORGANISM(S): Drosophila Melanogaster (ncbitaxon:7227) 
2017-10-25 | MSV000081643 | MassIVE
ProteomicsMudPIT analyses of the proteins purified by in vitro dCas9-targeted chromatin IP of telomere sequences in HeLa cells
We used a reverse chromatin immunoprecipitation (ChIP) method that takes advantage of the RNA-mediated DNA-targeting capability of Cas9 to efficiently and adaptably isolate specific genomic regions and their associated protein factors. By using purified recombinant catalytically-dead Cas9 (dCas9) co...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-10-25 | MSV000081645 | MassIVE
ProteomicsSingle-copy locus proteomics of early- and late-firing DNA replication origins identifies a role of Ask1/DASH complex in replication timing control
The chromatin at origins of replication is thought to influence DNA replication initiation in eukaryotic genomes. However, it remains unclear how the chromatin composition controls the firing of early-efficient (EE) or late-inefficient (LI) origins. Here, we used site-specific recombination and sing...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2023-02-16 | PXD032930 | Pride
Locus-specific chromatin isolation  site-specific recombination  affinity purification  dna replication origin  replication timing  replication efficiency  origin chromatin structure  dash complex  ask1 protein  microtubule cytoskeleton 
TranscriptomicsOpen chromatin in human pancreatic islets (FAIRE-seq) - Appendix to E-GEOD-17616
An appendix to the published Gaulton et al. work (PMID: 20118932; E-GEOD-17616). In the original paper, the authors note that samples 1 and 2 are not as pure as the third sample. This appendix provides FAIRE-Seq data obtained from a purified islet sample to replace the problematic published data. Th...
ORGANISM(S): Homo sapiens 
2014-12-23 | E-MTAB-3199 | biostudies-arrayexpress
TranscriptomicsA map of open chromatin in human pancreatic islets
High-throughput sequencing of genomic regions isolated using FAIRE (Formaldehyde-assisted isolation of regulatory elements) from three purified pancreatic islet samples For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCO...
ORGANISM(S): Homo sapiens 
2010-01-31 | E-GEOD-17616 | biostudies-arrayexpress
UnknowndCas9-targeted locus-specific protein isolation method identifies histone gene regulators.
Not available
S-EPMC5866577 | biostudies-literature
UnknownLocus-specific ChIP combined with NGS analysis reveals genomic regulatory regions that physically interact with the Pax5 promoter in a chicken B cell line.
Not available
S-EPMC5737561 | biostudies-literature
UnknownPurification of a specific native genomic locus for proteomic analysis.
Not available
S-EPMC3814360 | biostudies-literature
GenomicsAmplification of siRNA in Caenorhabditis elegans generates a transgenerational sequence-targeted histone H3 lysine 9 methylation footprint
Exogenous double-stranded RNA (dsRNA) has been shown to exert homology-dependent effects at the level of both target mRNA stability and chromatin structure. Using C. elegans undergoing RNAi as an animal model, we have investigated the generality, scope, and longevity of chromatin-targeted dsRNA effe...
ORGANISM(S): Caenorhabditis elegans 
2012-01-06 | E-GEOD-32631 | biostudies-arrayexpress
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