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ProteomicsIn vitro chromatin assembly - A quantitative proteomic analysis of in vitro assembled chromatin
Here, we use LC-MSMS and SWATH-MS to describe the kinetics of in vitro assembled chromatin supported by an embryo extract prepared from preblastoderm Drosophila melanogaster embryos. This system allows easy manipulation of distinct aspects of chromatin assembly such as post-translational histone mod...
ORGANISM(S): Drosophila melanogaster (Fruit fly) 
2016-01-27 | PXD003445 | Pride
Lc-msms Chromatin assembly Drosophila melanogaster 
ProteomicsA quantitative proteomic analysis of in vitro assembled chromatin
The structure of chromatin is critical for many aspects of cellular physiology and is considered to be the primary medium to store epigenetic information. It is defined by the histone molecules that constitute the nucleosome, the positioning of the nucleosomes along the DNA and the non-histone prote...
ORGANISM(S): Drosophila melanogaster (Fruit fly) 
2016-01-27 | PXD002537 | Pride
Acetylation  affinity proteomics  chromatin function or biology  label-free quantification   macromolecular assemblages 
Transcriptomicschromatin associated RNAs
RNA has been suggested to play a major role in the regulation of higher-order structures of chromatin. This study investigated chromatin-associated RNA (caRNA) in Drosophila melanogaster by applying high-throughput sequencing to RNA molecules that co-fractionate with chromatin. Using a cell-free in ...
ORGANISM(S): Drosophila melanogaster 
2014-06-19 | E-MTAB-1237 | biostudies-arrayexpress
ProteomicsDrosophila embryo extract assisted in vitro chromatin assembly in presence of foldamer
Drosophila preblastoderm embryo extract assisted chromatin assembly with or without 16mer DNA mimic. Pull down of chromatin fiber to reveal chromatin binders in the system.
ORGANISM(S): Drosophila melanogaster (Fruit fly) 
2023-09-07 | PXD039966 | Pride
Dna mimcs Qexactive hf Lc-ms In vitro chromatin assembly Drosophila embryo extract (drex) 
ProteomicsDNA mimicking 32mer foldamers interfere with in vitro chromatin assembly in drosophila embryo extract
Systematic study of the influence of different concentrations of DNA-mimicking foldamers (32mer) on the chromatin-bound bound proteome using an in vitro chromatin assembly extract
ORGANISM(S): Drosophila melanogaster (Fruit fly) 
2023-09-07 | PXD040158 | Pride
Dna mimcs Lc-ms Exploris 480 In vitro chromatin assembly Drosophila embryo extract (drex) 
TranscriptomicsRNA-seq of control siRNA, p150 siRNA and p60 siRNA transfected mES cells
Totipotent cells that resemble 2-cell stage embryos (2C-like cells) can arise with a very low frequency in ES cell cultures. Here we show that totipotent-like cells can be induced in vitro through the down-regulation of the chromatin assembly activity of CAF-1. Endogenous retroviruses and 2-cell sta...
ORGANISM(S): Mus musculus 
2015-08-02 | E-MTAB-2684 | biostudies-arrayexpress
GenomicsNucleosome mapping of Tetrahymena thermophila chromatin in vivo and in vitro
A conserved hallmark of eukaryotic chromatin architecture is the distinctive array of well-positioned nucleosomes downstream of transcription start sites (TSS). Recent studies indicate that trans-acting factors establish this stereotypical array. Here, we present the first genome-wide in vitro and i...
ORGANISM(S): Tetrahymena thermophila 
2015-07-30 | E-GEOD-64061 | biostudies-arrayexpress
ProteomicsIdentification of DNA-damage sensing factors in D.melanogaster
In order to identify protein involved in sensing DNA double strand breaks and recruiting the repair machinry, we performed in vitro assembly of chromatin on small circular and linear DNA templates, respectively. Proteins involved in chromatin assembly and sensing of free DNA ends were isolated and s...
ORGANISM(S): Drosophila melanogaster (Fruit fly) 
2019-10-14 | PXD012990 | Pride
Dna double strand break Repair factors Chromatin assembly 
TranscriptomicsA Basic Domain in the Histone H2B N-terminal Tail is Important for Nucleosome Assembly by FACT
Nucleosome assembly in vivo requires assembly factors, such as histone chaperones, to bind to histones and mediate their deposition onto DNA. In yeast, the essential histone chaperone FACT (FAcilitates Chromatin Transcription) functions in nucleosome assembly and H2A-H2B deposition during transcript...
ORGANISM(S): Saccharomyces cerevisiae 
2016-08-10 | E-GEOD-80831 | biostudies-arrayexpress
GenomicsBRG1 recruitment by transcription factors MITF and SOX10 defines a specific configuration of regulatory elements in the melanocyte lineage (ChIP-seq)
Microphthalmia-associated transcription factor (MITF) is the master regulator of the melanocyte lineage. By tandem affinity purification and mass spectrometry, we present a comprehensive characterisation of the MITF interactome comprising multiple novel cofactors involved in transcription, DNA repli...
ORGANISM(S): Homo sapiens 
2015-04-02 | E-GEOD-61965 | biostudies-arrayexpress
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