Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide transcriptomic analysis of Arabdiopsis mutants controling nuclear size in comparison to the wildtype

ABSTRACT: Genome-wide transcriptomic analysis of Arabdiopsis mutants controling nuclear size in comparison to the wildtype

PROVIDER: PRJNA417457 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR6264970_1.fastq.gz	Fastqsanger.gz
	SRR6264970_2.fastq.gz	Fastqsanger.gz
	SRR6264971_1.fastq.gz	Fastqsanger.gz
	SRR6264971_2.fastq.gz	Fastqsanger.gz
	SRR6264972_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 18

Similar Datasets

Genome-wide transcriptomic analysis of Arabdiopsis mutants controling nuclear size in comparison to the wildtype

Project description:We report genome-wide transcriptomic profile of 2 week-old Arabidopsis seedlings from pwo1 and crwn1 crwn2 mutants in comparison to the wildtype (Col-0)

2019-01-14 | GSE106615 | GEO

Nuclear cholesterol regulates nuclear size and DNA damage responses in the tumor hierarchy

Project description:Normal stem cells undergo morphologic, epigenetic, and metabolic changes during cellular differentiation. Here, we report that glioblastoma stem cells (GSCs) display smaller nuclear size than differentiated progeny. Leveraging differential gene expression and proteomics to discover potential mediators of nuclear size regulation, we found that GSCs are enriched for a nuclear lamina-localized sterol reductase, Lamin B Receptor (LBR). LBR bridges two functions, genome organization and cholesterol synthesis, of which nuclear cholesterol synthesis mediates LBR regulation of GSC nuclear size. Targeting LBR increased nuclear size and decreased GSC viability and tumor initiation. Mass spectrometry defined an LBR interactome in GSCs with mediators of DNA damage repair (DDR) and R-loop resolution, including DEAD-Box Helicase 5 (DDX5). Consistently, targeting LBR induced double-strand DNA breaks (DSBs) and P53-dependent DDR. Genetic LBR loss reduced DDX5 expression and increased R-loops; pharmacologic LBR sterol reductase inhibition phenocopied LBR loss, increasing R-loops and DSBs with synergy with irradiation to inhibit GSC survival. Together, we propose that LBR regulates nuclear cholesterol synthesis, which contributes to the small GSC nuclear sizes and promotes efficient DNA damage repair.

2025-05-03 | GSE246908 | GEO

Nucleocytoplasmic transport and membrane growth control nuclear size

Project description:How cells control the overall size of membrane-bound organelles is an important unanswered question of cell biology. Fission yeast cells maintain a nuclear size that is proportional to cellular size, resulting in a constant ratio between the nuclear and cellular volumes (N/C ratio). To shed light on nuclear size control we conducted a genome-wide visual screen of a fission yeast gene deletion collection for mutants altered in their N/C ratio, and found that defects in both nucleocytoplasmic mRNA transport and nuclear membrane proliferation alter the N/C ratio. Perturbing nuclear mRNA export causes general bulk accumulation of both mRNA and protein, and a N/C ratio increase which is dependent on new membrane synthesis. Dysregulation of nuclear membrane growth also results in an enlarged N/C ratio, and additionally generates an aberrant nuclear shape. We propose that both properly regulated nucleocytoplasmic transport and nuclear membrane growth are central for controlling nuclear size.

2017-06-05 | PXD004530 | Pride

Nuclear cholesterol regulates nuclear size and DNA damage responses in the tumor hierarchy

Project description:Nuclear cholesterol regulates nuclear size and DNA damage responses in the tumor hierarchy

| PRJNA1035086 | ENA

Comparison of human PRDM12 mutants D31Y and E172D with wildtype fibroblasts

Project description:Fibroblasts from PRDM12 patients and unaffected wildtype relatives were cultured until near confluency. The transcriptional profile of those cells was determined by mRNA sequencing and uncovered differential expression in several known pain and neurodevelopmental genes.

2015-06-03 | GSE61600 | GEO

SUN1/2 Controls Macrophage Polarization via Modulating Nuclear Size and Stiffness

Project description:SUN1/2 Controls Macrophage Polarization via Modulating Nuclear Size and Stiffness

| PRJNA1019379 | ENA

Cx32 surface expression (wildtype vs. mutants)

Project description:Cx32 wildtype and mutants (W3S, R22G) were expressed in HEK293F cells and subjected to surface biotinylation to check for expression level differences between the different conditions. A CFP control was conducted.

2023-08-08 | PXD033671 | Pride

Cell and nuclear size are associated with chromosomal instability and tumorigenicity in cancer cells that undergo whole genome doubling

Project description:Whole genome doubling (WGD) is a frequent event in cancer evolution associated with chromosomal instability, metastasis, and poor prognosis. While the genomic consequences of WGD are well documented, the effects of non-genetic alterations that accompany WGD, such as changes to cell and nuclear size, on tetraploid (4N) cancer cell physiology are less understood. Here, we show that cell and nuclear volume do not always scale with DNA content after WGD in cancer cells, resulting in 4N cells that differ in size. We find that small size is associated with enhanced cell fitness, mitotic fidelity, and tumorigenicity in 4N cancer cells and with poor patient survival in WGD-positive human cancers. Overall, these results suggest that cell and nuclear size contribute to the tumorigenic potential of 4N cancer cells and could be an important prognostic marker in human tumors that undergo WGD.

2025-05-28 | GSE297882 | GEO

Cx32 surface expression (wildtype vs. mutants) - HeLa cells

Project description:Cx32 wildtype and mutants (W3S, R22G) were expressed in HeLa cells and subjected to surface biotinylation to check for expression level differences between the different conditions. A CFP control was conducted.

2023-08-08 | PXD039379 | Pride

SUN1/2 Controls Macrophage Polarization via Modulating Nuclear Size and Stiffness

Project description:Alteration of the size and stiffness of the nucleus triggered by environmental cues are thought to be important for eukaryotic cell fate and function. Here we identify the nuclear envelope proteins SUN1/2 as mechano-regulators of the nucleus during M1 polarization of the macrophage. Specifically, we show that LPS treatment decreases the protein levels of SUN1/2 in a CK2-bTrCP-dependent manner to shrink and soften the nucleus, therefore altering the chromatin accessibility for M1-associated gene expression.

2023-09-28 | GSE243684 | 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