Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Deduction of proportional contributions of histone-modification-related DNA from various tissues in plasma

ABSTRACT: Deduction of proportional contributions of histone-modification-related DNA from various tissues in plasma

PROVIDER: EGAS00001006503 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

ChIP-seq of Drosophila melanogaster plasmatocytes agains various histone modifications

Project description:ChIP-seq of Drosophila melanogaster plasmatocytes agains various histone modifications

| PRJEB46189 | ENA

Expression data from human colorectal cancer tissues and the corresponding non-cancerous tissues [MeRIP-seq]

Project description:To identify the the functional roles and the pathophysiological contributions of the mRNA m6A modification in human colorectal carcinogenesis, we analysed the profile the landscape of the mRNA m6A modification in colorectal cancer tissues and the corresponding non-cancerous tissues.

2024-05-01 | GSE247632 | GEO

ChIP-chip of histone variants and modifications in S. pombe WT and various mutants

Project description:ChIP-chip of histone variants and modifications in A. thaliana WT and various mutants

2012-12-01 | GSE31071 | GEO

Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 lysine 36

Project description:Several lines of recent evidence support a role for chromatin in splicing regulation. Here we show that splicing can also contribute to histone modification, which implies a bidirectional communication between epigenetics and RNA processing. Genome-wide analysis of histone methylation in human cell lines and mouse primary T cells reveals that intron-containing genes are preferentially marked with H3K36me3 relative to intronless genes. In intron-containing genes, H3K36me3 marking is proportional to transcriptional activity, whereas in intronless genes H3K36me3 is always detected at much lower levels. Furthermore, splicing inhibition impairs recruitment of H3K36 methyltransferase HYPB/Setd2 and reduces H3K36me3, whereas splicing activation has the opposite effect. Moreover, the increase of H3K36me3 correlates with the length of the first intron, consistent with the view that splicing enhances H3 methylation. We propose that splicing is mechanistically coupled to recruitment of HYPB/Setd2 to elongating RNA Polymerase II. This experiment proposes to profile genome-wide binding profiles by ChIP-seq (Illumina, 36 bp tags) of RNA polymerase II (one biological replicate), the histone modification H3K36me3 (2 replicates) and a reference control input sample (genomic DNA after reverse cross-link, one replicate) in a human H1299 lung carcinoma cell line *** Raw data not provided for Samples GSM766322-GSM766324.

2011-07-25 | E-GEOD-30902 | biostudies-arrayexpress

Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification

Project description:Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification

| PRJNA147047 | ENA

Genome wide analysis of binding regions for MYC, MYCN and various histone modifications using Cut&Run

Project description:Cut&Run analysis was performed in RPMI-8402 cells to analyze binding regions of MYC, MYCN and various histone modifications in normal culture conditions

2023-08-16 | GSE231963 | GEO

A unidirectional histone code in bidirectional promoters across cell types

Project description:Recent studies indicate that thousands of genes are expressed from bidirectional promoters (BDPs). Gene regulation at BDPs is poorly understood, in particular how the cell is able to regulate them differently. Here we investigate the effect of histone Modifications in BDP regulation. In this study, we model the gene activity using different gene expression assays, such as RNA-Seq, GRO-cap, and CAGE around the BDP transcription start sites (TSSs) using different histone modifications in various cell types. We develop a new statistical approach that links histone modifications to gene expression at BDPs. It improves over previous methods, because it is able to capture spatial dependencies of histone modifications along a promoter and leads to more interpretable results. We predict a general histone code that is independent of transcript orientation, cell type, and promoter configuration. The histone code at BDPs reveals that promoters are regulated unidirectionally, such that the majority of histone marks associated with gene expression occur downstream of the gene's TSS. By contrasting associations of histone marks with steady-state levels of capped RNAs in CAGE and nascent capped RNAs in GRO-cap, we show which histone marks have a preference for initiating polymerases and actively elongating polymerases. Using single-cell data we show that the bidirectional histone signal of activating marks is often due averaging of a heterogeneous cell population. Our results have implications for other experiments where the relationship between histone modification and gene initiation or gene elongation is investigated on a genome-wide scale.

| EGAS00001001656 | EGA

Dynamics and functional interplay of histone lysine butyrylation, crotonylation, and acetylation in rice under starvation and submergence

Project description:In this work, we detected lysinebutyrylation (Kbu) and crotonylation(Kcr) sites in rice histone proteins by mass spectrometry, and found both similar and specific acylation patterns compared with that in mammalian cells. Comparative analysis of genome-wide histone Kbu, Kcr, and H3K9ac in combination of RNA-sequencing revealed that a large number of rice genes are marked by both Kbu and Kcr, most of which overlap with H3K9ac and are active genes. Under starvation and submergence, Kbu andKcr appeared to be less dynamic than H3K9ac and the three marks displayed changes in different sets of genes. Kbu and Kcr seemed to have a function to poise stress-induced gene activation. The results suggest that histone Kbu and Kcr provide a platform for histone acetylation during gene activation and that the proportional mixture of distinct histone lysine acylations which are regulated by environmental cues and has functionally consequence in chromatin modification and gene expression in plants.

2018-09-08 | GSE111308 | GEO

Epigenomic profiling and transcriptomic profiling of LUAD patients tumor tissues and tumor adjacent tissues

Project description:To provide an in-depth understanding of the epigenomic heterogeneity of LUAD, we here investigated the H3K27ac histone modification profiles of tumors and adjacent normal lung tissues from 42 LUAD patients and explored the role of epigenetic alterations in LUAD progression. We also investigated transcriptomic alterations among 36 patients tumor tissues.

| EGAS00001005132 | EGA

Epigenome analyses reveal histone H4K20me3 and radiation related genes in NSCLC cell

Project description:Purpose: Radiotherapy is useful for non-small cell lung cancer (NSCLC) patients who cannot be treated surgically. Modification of histone proteins also occurs during radiotherapy, and affects gene expression. In this study, we assessed the effects of radiotherapy on histone H4K20me3 in NSCLC cells. Methods: NCI-H460 NSCLC cell line were subjected to gamma irradiation. To reveal H4K20me3-related genes, we conducted chromatin immunoprecipitation(ChIP) and ChIP-sequencing. Results: We evaluated the H4K20me3-related genes through ChIP-sequencing.

2020-05-12 | GSE133519 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data