Ontology highlight
ABSTRACT:
PROVIDER: PRJNA957486 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24222475_1.fastq.gz | Fastqsanger.gz | |||
| SRR24222475_2.fastq.gz | Fastqsanger.gz | |||
| SRR24222476_1.fastq.gz | Fastqsanger.gz | |||
| SRR24222476_2.fastq.gz | Fastqsanger.gz | |||
| SRR24222477_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Lysine crotonylation (Kcr) is a newly discovered post-translational modification (PTM) existing in mammalian. Here, we performed a global crotonylome analysis of rice (Oryza sativa L. japonica) using high accuracy nano-LC-MS/MS in combination with crotonylated peptide enrichment. A total of 1,265 lysine crotonylation sites were identified on 690 proteins in rice seedlings. Subcellular localization analysis revealed that 51% of the crotonylated proteins identified were predicted to be associated with chloroplasts. The photosynthesis-associated proteins were also mostly enriched in total crotonylated proteins. Furthermore, to assess the relevance between histone Kcr and the genome, we performed a genomic localization analysis of histone Kcr by ChIP-seq analysis. Of the 10,923 identified peak regions, the majority (86.7%) of the enriched peaks were located in genes, especially exons. Furthermore, the degree of histone Kcr modification was positively correlated with gene expression in genic regions. Compared with other published histone modification data, the Kcr was co-located with the active histone modifications. Interestingly, histone Kcr facilitated expression of genes with existing active histone modifications. In addition, 77% of histone Kcr modifications overlapped with DNase hypersensitive sites (DHSs) in intergenic regions of the rice genome, and might mark other cis-regulatory DNA elements which are different from IPA1, a transcription activator in rice seedling. Overall, our results provide a comprehensive understanding of the biological functions of the crotonylome and new active histone modification in transcriptional regulation in plants.
2018-07-23 | PXD008716 | Pride
Project description:Lysine crotonylation (Kcr) is a newly discovered post-translational modification (PTM) existing in mammals. A global crotonylome analysis was undertaken in rice (Oryza sativa L. japonica) using high accuracy nano-LC-MS/MS in combination with crotonylated peptide enrichment. A total of 1,265 lysine crotonylation sites were identified on 690 proteins in rice seedlings. Subcellular localization analysis revealed that 51% of the crotonylated proteins identified were localized in chloroplasts. The photosynthesis-associated proteins were also mostly enriched in total crotonylated proteins. In addition, a genomic localization analysis of histone Kcr by ChIP-seq was performed to assess the relevance between histone Kcr and the genome. Of the 10,923 identified peak regions, the majority (86.7%) of the enriched peaks were located in gene body, especially exons. Furthermore, the degree of histone Kcr modification was positively correlated with gene expression in genic regions. Compared with other published histone modification data, the Kcr was co-located with the active histone modifications. Interestingly, histone Kcr facilitated expression of genes with existing active histone modifications. In addition, 77% of histone Kcr modifications overlapped with DNase hypersensitive sites (DHSs) in intergenic regions of the rice genome, and might mark other cis-regulatory DNA elements which are different from IPA1, a transcription activator in rice seedlings. Overall, our results provide a comprehensive understanding of the biological functions of the crotonylome and new active histone modification in transcriptional regulation in plants.
2018-09-20 | PXD010376 | Pride
Project description:The centromere is defined by the presence of a centromere-specific histone H3 variant, CENH3. Establishment and maintenance of the centromeric chromatin (CEN chromatin) is determined by poorly understood epigenetic mechanisms. Interestingly, CEN chromatin in several eukaryotes showed euchromatic characteristics although being embedded within pericentromeric heterochromatin. Specifically, H3K4me2 appeared to be a unique histone modification mark associated with animal centromeres. We developed a genomic tiling array for four fully sequenced rice centromeres. A ChIP-chip approach was used to study the patterns of several euchromatic histone modification marks, including H3K4me2, H3K4me3, H3K36me3, and H3K4K9a, associated with rice centromeres. We demonstrate that the CENH3 subdomains within the four centromeres are depleted with the four histone H3 marks. The vast majority of the four histone marks were associated with the genes located in the H3 subdomains within the centromeric cores. Genes in the centromeres showed similar histone modification patterns as those located outside of the centromeres. Thus, the euchromatic characteristics of rice CEN chromatin are trademarks of the transcribed sequences embedded in the H3 subdomains of the centromeres. We propose that the constitutively expressed genes located in rice centromeres may provide a barrier for loading of CENH3 into the H3 subdomains. The separation of CENH3 into the H3 subdomains is favorable for the three dimensional structure and its associated function of rice centromeres. We developed a genomic tiling array that covers four rice centromeres (Cen4, Cen5, Cen7, and Cen8) using the NimbleGen 3x720K array based on the NimbleGen HD2 platform. We used four antibodies (H3K4me3, H3K4me2, H3K36me3, H3K4K9ac) to perform ChIP-chip experiments. ChIP was conducted using leaf tissue from two-week old rice seedlings. We have 3 biological replicates for each antibody and 6 technological replicates of hybridization with position exchange on the array. Thus, each histone modification included 18 hybridization experiments.
2011-11-09 | E-GEOD-29597 | biostudies-arrayexpress
Project description:The centromere is defined by the presence of a centromere-specific histone H3 variant, CENH3. Establishment and maintenance of the centromeric chromatin (CEN chromatin) is determined by poorly understood epigenetic mechanisms. Interestingly, CEN chromatin in several eukaryotes showed euchromatic characteristics although being embedded within pericentromeric heterochromatin. Specifically, H3K4me2 appeared to be a unique histone modification mark associated with animal centromeres. We developed a genomic tiling array for four fully sequenced rice centromeres. A ChIP-chip approach was used to study the patterns of several euchromatic histone modification marks, including H3K4me2, H3K4me3, H3K36me3, and H3K4K9a, associated with rice centromeres. We demonstrate that the CENH3 subdomains within the four centromeres are depleted with the four histone H3 marks. The vast majority of the four histone marks were associated with the genes located in the H3 subdomains within the centromeric cores. Genes in the centromeres showed similar histone modification patterns as those located outside of the centromeres. Thus, the euchromatic characteristics of rice CEN chromatin are trademarks of the transcribed sequences embedded in the H3 subdomains of the centromeres. We propose that the constitutively expressed genes located in rice centromeres may provide a barrier for loading of CENH3 into the H3 subdomains. The separation of CENH3 into the H3 subdomains is favorable for the three dimensional structure and its associated function of rice centromeres.
2011-11-09 | GSE29597 | GEO
Project description:ChIP-seq targeting the H3K27ac histone modification in cohesin-mutated (STAG2 or RAD21 mutation) and cohesin wildtype (CTRL-AMLs) AMLs.
| EGAD00001011204 | EGA
Project description:The molecular signature at histone H3K4 involved in epigenetic regulation of normal (MCF10A) and transformed (MCF7, MDA-MB-231) breast cells using ChIP-Seq technology. This study examines the dynamic distribution of H3K4me3 and H3K4ac histone modification associated with active chromatin to provide an understanding of the changes in epigenetic regulation associated with the unique breast cancer subtypes. H3K4me3 and H3K4ac histone modification study in normal (MCF10A) and transformed (MCF7, MDA-MB-231) breast cells using ChIP-Seq technology
2016-02-10 | E-GEOD-69377 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE26610: DNase I hypersensitive sites in two tissues of rice GSE26733: ChIP-seq to identify the positions of three histone modifications in the rice genome Refer to individual Series
2011-11-09 | E-GEOD-26734 | biostudies-arrayexpress
Project description:Examination of H3K27me3 histone modification in A549 cell line H3K27me3 ChiP-Seq
2015-12-11 | E-GEOD-75903 | biostudies-arrayexpress
Project description:ChIP-seq for histone modification in Sertoli cells
| PRJDB4293 | ENA
Project description:Epigenomic profiling by ChIP-seq is a prevailing methodology used to investigate chromatin-based regulation in biological systems, such as human disease, yet the lack of an empirical methodology to normalize amongst experiments has limited the usefulness of this technique. Here we describe a “spike-in” normalization method that allows the quantitative comparison of histone modification status across cell populations using defined quantities of a reference epigenome. We demonstrate the utility of this method in measuring epigenomic changes following chemical perturbations and show how control normalization of ChIP-seq experiments enables discovery of disease-relevant changes in histone modification occupancy. ChIP-Seq of histone modifications H3K79me2 and H3K4me3 in human samples treated with EPZ-5676 with/without reference epigenome spike-in.
2014-10-30 | E-GEOD-60104 | biostudies-arrayexpress