Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ChIP-seq for Col-0, atchz1ab, and arp6-1 using H2A.Z and H3 antibodies

ABSTRACT: ChIP-seq for Col-0, atchz1ab, and arp6-1 using H2A.Z and H3 antibodies

PROVIDER: PRJNA890636 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR21906836_1.fastq.gz	Fastqsanger.gz
	SRR21906836_2.fastq.gz	Fastqsanger.gz
	SRR21906837_1.fastq.gz	Fastqsanger.gz
	SRR21906837_2.fastq.gz	Fastqsanger.gz
	SRR21906838_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 18

Similar Datasets

ChIP-seq for Col-0, atchz1ab, and arp6-1 using H2A.Z and H3 antibodies

Project description:To investigate the influence of the AtChz1A/B and ARP6 in H2A.Z incorporation, we analysed genome-wide H2A.Z density in the mutant and wild-type by ChIP-seq. We then performed H2A.Z occupancy analysis using data obtained from ChIP-seq of 3 different plants including mutants and wild-type.

2023-04-01 | GSE215800 | GEO

ChIP-Seq of H2A.Z and H3

Project description:ChIP-Seq of H2A.Z and H3

| PRJNA649226 | ENA

Genome-wide maps of H3 and H2A.Z RITE ChIP-sequencing

Project description:We performed ChIP-sequencing for both H2A.Z and H3 RITE after 4 hours in G1-arrest. In addition, we report H2A.Z and H3 ChIP-sequencing data for samples of replicating cells.

2018-05-01 | GSE85031 | GEO

RNA-seq for Col-0, atchz1ab, hta9-1hta11-2, atchz1ab hta9-1hta11-2, arp6-1, atchz1ab arp6-1

Project description:To investigate the effect of the interaction between the AtChz1A/B, H2A.Z and ARP6, we analysed differentially expressed genes compared to the mutant and wild-type by RNA-seq. We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 different plants including mutants and wild-type.

2023-04-01 | GSE215799 | GEO

Chromatin-remodeling factor OsINO80 regulate H2A.Z incorporation [anti-H2A.Z & H3 ChIP-seq]

Project description:Chromatin-remodeling factor OsINO80 regulate H2A.Z incorporation [anti-H2A.Z & H3 ChIP-seq]

| PRJNA753508 | ENA

Methyl-CpG-binding domain 9 (MBD9) is required for H2A.Z incorporation into chromatin at a subset of H2A.Z-enriched regions in the Arabidopsis genome

Project description:The SWR1 chromatin remodeling complex, which deposits the histone variant H2A.Z into nucleosomes, has been characterized in yeast and animals but had not been purified from plants. We used the conserved SWR1 subunit ACTIN RELATED PROTEIN 6 (ARP6) as bait in tandem affinity purification experiments to isolate associated proteins from Arabidopsis thaliana. We identified all 11 subunits found in yeast SWR1 and the homologous mammalian SRCAP complexes, demonstrating that this complex is conserved in plants. We also identified several additional proteins not previously associated with SWR1, including Methyl-CpG-BINDING DOMAIN 9 (MBD9). Since mbd9 mutant plants were phenotypically similar to arp6 mutants, we further explored a potential role for MBD9 in H2A.Z deposition. We found that MBD9 is required for proper H2A.Z incorporation at thousands of discrete sites, which represent a subset of the regions normally enriched with H2A.Z. Genetic analyses showed that arp6;mbd9 double mutants have far more severe phenotypes than either single mutant. In conjunction with the finding that MBD9 does not appear to be a core subunit of the Arabidopsis SWR1 complex, this suggests that MBD9 also has important roles beyond H2A.Z deposition. Our data establish the SWR1 complex as being conserved across eukaryotes and also provide new insights into the mechanisms that target H2A.Z to chromatin.

2018-08-31 | GSE117391 | GEO

MPK4 mediated phosphorylation of PIF4 controls thermosensing by regulation of H2A.Z deposition in Arabidopsis

Project description:Plants have the ability to perceive a slight upsurge in ambient temperature and respond by undergoing morphological changes, such as elongated hypocotyls and early flowering. The dynamic functioning of PHYTOCHROME INTERACTING FACTOR4 (PIF4) in thermomorphogenesis has been well established, although the regulatory pathway involved in thermosensing is not deciphered completely. In our study, we demonstrate that an increase in temperature from 22˚C to 28˚C induces the phosphorylation of PIF4 by MITOGEN-ACTIVATED PROTEIN KINASE 4 (MPK4) which shows high expression and activation at 28˚C. Phosphorylated PIF4 represses the expression of ACTIN-RELATED PROTEIN 6 (ARP6) that is required for mediating histone variant H2A.Z deposition at its target gene loci. We demonstrate that variation of ARP6 expression in PIF4 phosphor -null and phosphor-mimetic seedlings affects hypocotyl growth and flowering at 22˚C and 28˚C. Further, we show that change in ARP6 expression affects H2A.Z deposition at the loci of genes involved in hypocotyl elongation using PIF4 phosphor -null and phosphor-mimetic seedlings. Interestingly, the expression of MPK4 is also controlled by H2A.Z deposition in temperature dependent manner. Taken together, our findings highlight the cumulative molecular interplay between MPK4, PIF4, and chromatin modification by ARP6-mediated H2A.Z deposition as a regulatory mechanism of thermosensing.

2024-08-01 | GSE253263 | GEO

Total RNA sequencing of progenies of Col-0 grafted on msh1; Col-0 grafted on dcl2,3,4,msh1; Col-0 grafted on Col-0 in Arabidopsis [msh1_graft_leaf_RNA-seq]

Project description:Col-0 floral stem was grafted on the msh1 mutant (Col-0/msh1); on the dcl2,3,4,msh1 quadruple mutant (Col-0/dcl2,3,4,msh1); on Col-0 (Col-0/Col-0). Seeds were collected from the grafted Col-0 scion after grafts were established. Seed coming from the graft then were grown on the peat mix, leaf tissue was collected at the bolting and used for the total RNA sequencing.

2020-09-20 | GSE152565 | GEO

ChIP-seq for Col-0 and pif4 using H3K9ac/H4K5ac antibodies.

Project description:ChIP-seq for Col-0 and pif4 using H3K9ac/H4K5ac antibodies.

| PRJNA1063617 | ENA

ChIP-seq for OsINO80 location using YFP antibody, and ChIP-seq for WT and osino80 using H3, H2A, H2A.Z, H2Aub, H3K9me2, H3K4me2, H3K4me3, H3K27me3, and H3K36me3 antibodies

Project description:To investigate the effect of the OsINO80, we analysed OsINO80 binding regions and analysed genome-wide H3, H2A, H2A.Z, H2Aub, H3K9me2, H3K4me2, H3K4me3, H3K27me3, and H3K36me3 in the mutant and WT by ChIP-seq.

2024-04-10 | GSE225484 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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