Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Set1 targets gene with essential identity and tumor suppressing functions in planarian stem cells. Mnase-ChIP was used to validate a wide histone H3K4me3 peak width signature.

ABSTRACT: Previous publications have reported the significance of a wide histone H3K4me3 signature at essential genes in many organisms and cell types. Most of these published datasets were produced using cross-linking ChIP-seq, in which the chromatin was chemically cross-linked using formadehyde and then mechanically sheared with sonication. Here we use Mnase-ChIP, a non-cross-linking method that fractionates chromatin using the enzyme micrococcal nuclease, to show that this wide H3K4me3 signature is not a technical artifact of cross-linking ChIP.

ORGANISM(S): Schmidtea mediterranea Drosophila melanogaster

PROVIDER: GSE180591 | GEO | 2021/07/26

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

The S-adenosyl-homosteine hydrolase inhibitor DZNeP unspecifically affects histone methylation patterns in embryos and results in developmental aberrations

Project description:3-deazaneplanocin A (DZNeP) is a promising cancer drug affecting the methylation status of histone lysine residues. To investigate the specificity and mode of action of DZNeP, zebrafish embryos displaying high histone methyltransferase activity were cultured with DZNeP and histone methylation (H3K4me3, H3K9me3, H3K27me3) was mapped by ChIP-chip genome-wide promoter at post-MBT stage (5.3 hpf) . We used a custom 2.1M probe HD promoter array (Nimblegen) for ChIP and input DNA hybridization. Peak detection was done using MA2C with P=10e-4 as cutoff. ChIP-chip experiments were performed from chromatin prepared by sonication after formaldehyde cross-linking, from embryos are the indicated developmental stages and ChIP DNA was hybridized onto the aforementioned Nimbegen promoter arrays.

2014-11-21 | E-GEOD-53209 | biostudies-arrayexpress

Marking of the genome by H3K4 methylation prior to embryonic gene activation

Project description:Early zebrafish embryo development proceeds first from a maternally transcribed and stored mRNAs, and zygotic gene activation (ZGA) is initiated at the mid-blastula transition (MBT; 1000-cell stage), 3.3 h post-fertilization. Very little is known on how the zygotic genome is programmed for transcriptional activation at the MBT. To start addressing this issue, we have mapped by ChIP-chip genome-wide promoter histone methylation (H3K4me3, H3K9me3, H3K27me3, H3K36me3) and RNA Pol II profiles before ZGA (256-cell stage; 2.5 hpf), during ZGA (MBT; 3.5 hpf)) and after ZGA (Post-MBT; 5.3 hpf) . We used a custom 2.1M probe HD promoter array (Nimblegen) for ChIP and input DNA hybridization. Peak detection was done using MA2C with P=10e-4 as cutoff. ChIP-chip experiments were performed from chromatin prepared by sonication after formaldehyde cross-linking, from embryos are the indicated developmental stages and ChIP DNA was hybridized onto the aforementioned Nimbegen promoter arrays.

2011-12-02 | E-GEOD-27314 | biostudies-arrayexpress

Set1 targets gene with essential identity and tumor suppressing functions in planarian stem cells. Mnase-ChIP was used to validate a wide histone H3K4me3 peak width signature.

Project description:Set1 targets gene with essential identity and tumor suppressing functions in planarian stem cells. Mnase-ChIP was used to validate a wide histone H3K4me3 peak width signature.

| PRJNA748752 | ENA

two steps cross-linking ChIP-seq

Project description:two steps cross-linking ChIP-seq

| PRJNA794157 | ENA

single step cross-linking ChIP-seq

Project description:single step cross-linking ChIP-seq

| PRJNA794167 | ENA

Two steps cross-linking LCL ChIP-seq

Project description:Two steps cross-linking LCL ChIP-seq

| PRJNA795780 | ENA

Single step cross-linking LCL ChIP-seq

Project description:Single step cross-linking LCL ChIP-seq

| PRJNA795781 | ENA

HeLa mRNA interactome

Project description:Pull-down of poly(A)-mRNA cross linked proteins using two cross-linking methods (conventional cross-linking and PAR-cross-linking) to identify all mRNA-binding proteins (GO:0003729). The provided data is quantitative proteomic data for comparison of cross-linking and control samples.

2012-08-14 | E-MTAB-869 | biostudies-arrayexpress

Peak Width of Skeletonized Water Diffusion MRI in the Neonatal Brain.

Project description: Not available

| S-EPMC7146826 | biostudies-literature

Epigenetic regulation by chromatin activation mark H3K4me3 in primate progenitor cells within adult neurogenic niche [ChIP-seq]

Project description:Histone 3 lysine 4 trimethylation (H3K4me3) is known to be associated with transcriptionally active or poised genes and required for postnatal neurogenesis within the subventricular zone (SVZ) in the rodent model. Previous comparisons have shown significant correlation between baboon (Papio anubis) and human brain. In this study, we demonstrate that chromatin activation mark H3K4me3 is present in undifferentiated progenitor cells within the SVZ of adult baboon brain. To identify the targets and regulatory role of H3K4me3 within the baboon SVZ, we developed a technique to purify undifferentiated SVZ cells while preserving the endogenous nature without introducing culture artifact to maintain the in vivo chromatin state for genome-wide studies (ChIP-Seq and RNA-Seq). Overall, H3K4me3 is significantly enriched for genes involved in cell cycle, metabolism, protein synthesis, signaling pathways, and cancer mechanisms. Additionally, we found elevated levels of H3K4me3 in the MRI-classified SVZ-associated Glioblastoma Multiforme (GBM), which has a transcriptional profile that reflects the H3K4me3 modifications in the undifferentiated progenitor cells of the baboon SVZ. Our findings highlight the importance of H3K4me3 in coordinating distinct networks and pathways for life-long neurogenesis, and suggest that subtypes of GBM could occur, at least in part, due to aberrant H3K4me3 epigenetic regulation. SVZ H3K4me3 ChIP-seq profile of an adult baboon brain was generated by deep sequencing with Illumina HiSeq 2000.

2014-07-16 | E-GEOD-58530 | biostudies-arrayexpress

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