Segmental chromatin states
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA701668 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13700615_1.fastq.gz | Fastqsanger.gz | |||
| SRR13700615_2.fastq.gz | Fastqsanger.gz | |||
| SRR13700616_1.fastq.gz | Fastqsanger.gz | |||
| SRR13700616_2.fastq.gz | Fastqsanger.gz | |||
| SRR13700617_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 61 |
Similar Datasets
Project description:We profiled the chromatin accessibility, transcription factor binding, and gene expression in the homologous wing and haltere imaginal disc of Drosophila melanogaster, which are distinguished by the expression of the Hox protein Ultrabithorax (Ubx). Through the analysis of chromatin changes, we show Ubx has widespread effects on the chromatin landscape to specify cell identity.
2021-05-18 | GSE166714 | GEO
Project description:Chromatin Immunoprecipitation followed by sequencing (ChIP-seq) has been instrumental to our current view of chromatin structure and function. It allows genome-wide mapping of histone marks, which demarcate biologically relevant domains. However, ChIP-seq is an ensemble measurement reporting the average occupancy of individual marks in a cell population. Consequently, our understanding of the combinatorial nature of chromatin states relies almost exclusively on correlation between the genomic distributions of individual marks. Here, we report the development of Combinatorial-iChIP to determine the genome-wide co-occurrence of histone marks at single nucleosome resolution. By comparing to null model, we show that certain combinations of overlapping marks (H3K36me3 and H3K79me3) co-occur more frequently than expected by chance, while others (H3K4me3 and H3K36me3) do not, reflecting differences in the underlying chromatin pathways. We further use combinatorial-iChIP to illuminate aspects of the Set2-RPD3S pathway. This approach promises to improve our understanding of the combinatorial complexity of chromatin. Combinatorial iChIP in yeast.
2016-08-02 | E-GEOD-84240 | biostudies-arrayexpress
Project description:Goal of this project was the identification of chromatin interacting proteins whose binding is differentially regulated by various combinatorial chromatin modifications found in different chromatin states such as promoters, enhancers and heterochromatin. To achieve this, recombinant modified nucleosomes representing different chromatin states were assembled from canonical histones, H2A.Z and modified ligated H3/H4 histone proteins and biotinylated nucleosomal DNAs. Assembled nucleosomes were immobilized on streptavidin-coated beads via biotinylated di-nucleosomal 601 DNA and used for nucleosome affinity purifications to identify proteins regulated by chromatin modifications from SILAC-labelled HeLaS3 nuclear extracts (Arg10 and Lys8). SILAC affinity purifications were carried out in "forward" (heavy extract on modified nucleosome and light extract on unmodified nucleosome) and "reverse" (light extract on modified nucleosome and heavy extract on unmodified nucleosome) label-swap experiments and protein abundances were quantified by MaxQuant. Initial trial experiments with biotinylated mono-, di- and tetra- 601 nucleosomes are also deposited along with the data for the di-nucleosome experiments. See also: Bartke et al., 2010. Nucleosome-interacting proteins regulated by DNA and histone methylation. Cell 143, 470–484; doi:10.1016/j.cell.2010.10.012. The H4K20me2 samples from this experiment were previously deposited with identifier PXD009281. These were published in: Nakamura et al., 2019. H4K20me0 recognition by BRCA1-BARD1 directs homologous recombination to sister chromatids. Nature Cell Biology 21, 311–318; doi: 10.1038/s41556-019-0282-9.
2023-12-12 | PXD018966 | Pride
Project description:Under continuous, glucose-limited conditions, budding yeast exhibit robust metabolic cycles associated with major oscillations of gene expression and metabolic state. However, how such fluctuations might be coordinately linked to changes in chromatin status is less well understood. Here, we examine the correlated genome-wide transcription and chromatin states across the yeast metabolic cycle (YMC) at unprecedented temporal resolution, revealing a "just in time supply chain" by which specific cellular processes such as ribosome biogenesis are coordinated in time with remarkable precision. We identify distinct chromatin and splicing patterns associated with different gene categories and determine the relative timing of chromatin modifications to maximal transcription. Additionally, we interrogate chromatin modifier occupancy and observe subtly distinct spatial and temporal patterns compared to the modifications themselves. Furthermore, we identify multiple lysine mutants in H3 or H4 tails that disrupt metabolic cycling, supporting a potentially cooperative role of histone modifications in the YMC. 16 time points RNA-seq and ChIP-seq of 8 histone marks over one metabolic cycle, 14 time points ChIP-seq of 3 chromatin modifiers over one metabolic cycle
2014-08-31 | E-GEOD-52339 | biostudies-arrayexpress
Project description:Chromatin States in Murine Spermatogonia
| PRJNA810498 | ENA
Project description:Chromatin modifications instruct genome function through spatiotemporal recruitment of regulatory factors to the genome. However, how these modifications define the proteome composition at distinct chromatin states remains to be fully characterized. Here, we made use of natural protein domains as modular building blocks to develop engineered chromatin readers (eCRs) selective for histone and DNA modifications. By stably expressing eCRs in mouse embryonic stem cells and measuring their subnuclear localisation, genomicdistribution and histone-PTM-binding preference, we first demonstrate their applicability as selective chromatin binders in living cells. Finally, we exploit the binding specificity of eCRs to establish ChromID, a new method for chromatin-dependent proteome identification based on proximity biotinylation. We use ChromID to reveal the proteome at distinct chromatin states in mouse stem cells, and by using a synthetic dual-modification reader, we furthermore uncover the protein composition at bivalent promoters marked by H3K4me3 and H3K27me3. These results highlight the applicability of ChromID as novel method to obtaina detailed view of the protein interaction network determined by the chemical language on chromatin.
2020-04-30 | PXD014483 | Pride
Project description:Chromatin states in the Arabidopsis seedlings
| PRJEB15549 | ENA
Project description:This study centered on using a custom made Nimblegen aCGH chip that targeted all segmental duplications in the canine genome to identify associated CNVs. A total of 19 hybridizations were performed in a panel of diverse dogs and a single wolf. Using computational approaches all segmental duplications were identified in the canFam2 genome of the dog. A custom aCGH chip was then built that densely interrogated these segmental duplications for CNVs in a panel of diverse dog breeds and a single wolf.
2010-05-17 | E-GEOD-13266 | biostudies-arrayexpress
Project description:The extent and nature of the changes in epigenome and their association with cancer progression are not completely understood. Here we profiled 35 epigenetic modifications and gene expression to understand changes in the epigenome during melanoma progression using a primary cell line based melanoma progression model representing non-tumorigenic and tumorigenic states based on constitutively active BRAF and PTEN knockdown. Identification of chromatin states based on the combinatorial and spatial pattern of the histone modifications revealed specific changes in them during transition to tumorigenesis. Major changes in chromatin states comprised of loss of histone acetylation events in combination with H3K4 methylation. These chromatin state changes primarily enriched for enhancers and promoter states. The putative gene targets of these enhancers and promoters that changed genes were most enriched in cancer-regulatory pathways including cell cycle, apoptosis, cell adhesion and immune response. A ChIP-String assay was used to validate some of the chromatin state changes in human tumor samples.
2017-04-24 | GSE58953 | GEO