Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE215799 | GEO | 2023/04/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

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

Expression in arp6 and swr1 deletion mutants

Project description:Actin-related proteins are ubiquitous components of chromatin remodelers, and are conserved from yeast to man. We have examined the role of the budding yeast actin-related protein Arp6 in gene expression, both as a component of the SWR1 complex (SWR-C) and in its absence. We mapped Arp6-binding sites genome-wide using chromatin immunoprecipitation in mutant and wild-type cells. We find that the majority of Arp6-binding sites in euchromatin coincide with binding sites of Swr1, the catalytic subunit of SWR-C, and with the histone H2A variant Htz1. However, the remaining Arp6 binding in telomeres, centromeres, and the promoters of ribosomal protein (RP) genes are independent of Swr1 and Htz1 deposition. We show that Arp6 can position chromatin at nuclear pores, and is required for the pore association of the RP genes to which it binds. This anchoring is also independent of Swr1. Loss of Arp6, but not Htz1, leads to an up-regulation of RP genes and loss of relocalization. This is in contrast to the Htz1-mediated pore-association of GAL1, for which loss of Arp6 impairs activation. Given that Arp6 is required for SWR-C dependent deposition of Htz1, we conclude that Arp6 contributes to both H2AZ-dependent and H2AZ-independent association with nuclear pores and subsequent effects on gene expression. These data illustrate how nuclear actin-related proteins contribute to the long-range organization of chromatin domains in the interphase nucleus. Four replicates for the arp6 deletion mutant and three replicates for the swr1 deletion mutant compared to wild-type.

2010-05-01 | E-GEOD-17780 | biostudies-arrayexpress

Expression in arp6 and swr1 deletion mutants

2010-05-01 | GSE17780 | GEO

ChIP-seq for HA-HTR5/Col-0 and Col-0 using HA antibody

Project description:To investigate the deposition of HTR5 in Arabidopsis, we analysed genome-wide HTR5 density in the wild-type Col-0 by ChIP-seq. We then performed HTR5 occupancy analysis using data obtained from ChIP-seq of 3 different plants including HA-HTR5/Col-0 and Col-0. Col-0 acted as negative control.

2023-04-01 | GSE223308 | GEO

The SWR1 Complex Regulates Active DNA Demethylation in Arabidopsis

Project description:Using BS-Seq to provide single-base resolution of DNA methylation status in 35S-SUC2 WT and antisilencing mutants (arp6, pie1, h2a.z, idm1, and ros1)

2020-12-06 | GSE107751 | GEO

Arabidopsis thaliana Col-0 wild type, deg10-1, deg10-2 and catr3-1 root proteome

Project description:Deg/HtrA proteases are important factors of the cellular protein quality control system, but little is know about their function in mitochondria. DEG10 loss-of-function mutants were impaired in root elongation at elevated temperature and reduced seed set in field trials. This study analysed the root proteome of two DEG10 loss-of-function mutants, deg10-1 and deg10-2, in comparison to wild type and the catr3-1 mutant (which is a second mutation in deg10-1).

2019-06-06 | PXD007204 | Pride

Arabidopsis buds: ahl16 vs. Col-0

Project description:Transcriptional profiling of Arabidopsis buds comparing ahl16 mutants with wild type (Col-0 ecotype). Goal was to determine the differential expression genes between the buds of mutant and wild type.

2014-04-04 | GSE56497 | GEO

MethylC-Seq of Ws background wild-type (WT), ape1l-1 (Ws background), arp-1 (Col-0 background) and zdp-1 (Col-0 background) mutants

Project description:Using MethylC-Seq to provide single-base resolution of DNA methylation status in Ws background wild-type (WT), ape1l-1 (Ws background), arp-1 (Col-0 background) and zdp-1 (Col-0 background) mutants

2014-11-21 | GSE52983 | GEO

Transcriptome comparison of the irt1-2 mutant (pam42) and the corresponding wild type (Col-0)

Project description:IRT1 is the root high-affinity Fe uptake system. Despite severe Fe deficiency symptoms and reduced Fe levels in the shoots of irt1 mutants, we find that root Fe concentrations are higher in the irt1-2 mutant than in the wild type, unexpectedly. The goal of this experiment was to identify candidate transcripts contributing to the observed alteration in root-to-shoot Fe partitioning of irt1. We analysed gene expression in shoots and roots of the wild type grown under control conditions, the wild type exposed to severe Fe deficiency for 5 d, as well as of the irt1-2 (pam42) mutant grown under control conditions.

2021-03-31 | GSE166269 | GEO

H2A.Z ChIP-seq of WT, ros1-14, idm1-9, arp6-4 and pie1-6

Project description:Using ChIP-seq to study the deposition of H2A.Z in different anti-silencing mutants

2020-12-06 | GSE107750 | GEO