Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mus musculus

ABSTRACT: DNA methylomes at base resolution of mouse embryonic fibroblasts in G1 and G2 phase of cell cycle

PROVIDER: PRJNA358740 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR5130340_1.fastq.gz	Fastqsanger.gz
	SRR5130340_2.fastq.gz	Fastqsanger.gz
	SRR5130339_1.fastq.gz	Fastqsanger.gz
	SRR5130339_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

DNA methylomes at base resolution of mouse embryonic fibroblasts in G1 and G2 phase of cell cycle

Project description:Dramatic change in DNA methylation patterns and levels both globally and/or locus-specifically is associated with the process of cell lineage specification and somatic reprogramming. We found the expression of DNA methyltransferase 1 (Dnmt1), the enzyme that maintains 5-methylcytosine (5mC) after DNA replication, is tightly regulated by the progression of cell cycle. Upregulation of Dnmt1 was observed in cells with shortened G1 and G2 phase. We hypothesize that 5mC level is not completely recovered by Dnmt1 immediately after DNA replication. In the attempt to clarify DNA methylation status before and after DNA replication, we performed Whole Genome Bisulfite Sequencing (WGBS) to map genome-wide DNA methylation separately in G1 and G2 phase of mouse embryonic fibroblasts (MEFs). Cells of different cell cycle phases were sorted by flow cytometry after Propidium iodide (PI) staining. We find an average of 2% decrease of global DNA methylation in G2 phase compared with G1, with the trend more magnificent in high CpG density regions. Generally, the results indicate that the G1 phase of cell cycle is an important time window for the stability of DNA methylation inheritance.

2017-10-13 | GSE92903 | GEO

Gene expression signatures in cell cycle sorted cells [HeLa_mRNA_array]

Project description:For the further examination of cell cycle dependent gene expression profile, DNA content based fluorescence activated cell sorting (cell cycle sort) was performed on human transformed cancer cell lines and primary, untransformed fibroblasts. Phase-dependent gene expression profiling was performed on G1, S and G2 phases. Results were validated by quantitative real-time PCR. Phase-dependent gene expression profiling was performed on sorted human cancer (cervical - HeLa and adrenocortical - NCI-H295R) cells and primary untransformed fibroblasts (HDFa). G1, S and G2 phases were successfully sorted and analyzed. HeLa_mRNA dataset

2016-05-28 | E-GEOD-73196 | biostudies-arrayexpress

Gene expression signatures in cell cycle sorted cells [HDFa_mRNA_array]

2016-05-28 | GSE73198 | GEO

Gene expression signatures in cell cycle sorted cells [HeLa_mRNA_array]

2016-05-28 | GSE73196 | GEO

MiRNA signatures in cell cycle sorted cells [H295R_miRNA_array]

Project description:For the further examination of cell cycle dependent miRNA expression profile, DNA content based fluorescence activated cell sorting (cell cycle sort) was performed on human transformed cancer cell lines and primary, untransformed fibroblasts. Phase-dependent miRNA expression profiling was performed on G1, S and G2 phases. Results were validated by quantitative real-time PCR.

2016-05-28 | GSE73258 | GEO

MiRNA signatures in cell cycle sorted cells [HDFa_miRNA_array]

2016-05-28 | GSE73257 | GEO

Gene expression signatures in cell cycle sorted cells [H295R_mRNA_array]

2016-05-28 | GSE73256 | GEO

MiRNA signatures in cell cycle sorted cells [HeLa_H295R_miRNA_seq]

Project description:For the further examination of cell cycle dependent miRNA expression profile, DNA content based fluorescence activated cell sorting (cell cycle sort) was performed on human transformed cancer cell lines. Phase-dependent miRNA expression profiling was performed on G1, S and G2 phases. Results were validated by quantitative real-time PCR. Phase-dependent miRNA expression profiling was performed on sorted human cancer (cervical - HeLa, adrenocortical - NCI-H295R) cells). G1, S and G2 phases were successfully sorted and analyzed.

2016-05-28 | E-GEOD-73200 | biostudies-arrayexpress

Overall reduction in 5hmC levels during the S phase of DNMT1-deficient mouse embryonic stem cells

Project description:DNA methylation is an essential for genome stability and mammalian embryonic development. DNA methyltransferase 1 (DNMT1) maintains cellular DNA methylation profile and its loss causes embryonic lethality. In this study, immunofluorescence staining, which can compare the difference between sister chromatids, were performed in mouse embryonic stem cells (ESCs) and suggest that the timing and region of de novo methylation by DNMT3 are restricted in DNMT1-deficient ESCs. To reanalyze the timing of de novo methylation by DNMT3, we collected cells from G1 to early S phases (called G1), cells in the mid-S phase, and cells in late S, G2, and M phases (called G2) by FACS, respectively. Among them, two cell populations, G1 and G2, were used for Me/hMeDIP-seq. As a result, the 5mC and 5hmC were globally decreased in the G2 cells.

2022-03-20 | GSE179515 | GEO

Identification of Primary Transcriptional Regulation of Cell-Cycle-Regulated Genes upon DNA Damage

Project description:The changes in global gene expression in response to DNA damage may derive from either direct induction or repression by transcriptional regulation or indirectly by synchronization of cells to specific cell cycle phases, such as G1 or G2. We developed a model that successfully estimated the expression levels of >400 cell-cycle-regulated genes in normal human fibroblasts based on the proportions of cells in each phase of the cell cycle. By isolating effects on the gene expression associated with the cell cycle phase redistribution after genotoxin treatment, the direct transcriptional target genes were distinguished from genes for which expression changed secondary to cell synchronization. Application of this model to ionizing radiation (IR)-treated normal human fibroblasts identified 150 of 406 cycle-regulated genes as putative direct transcriptional targets of IR-induced DNA damage. Changes in expression of these genes after IR treatment derived from both direct transcriptional regulation and cell cycle synchronization. Keywords: Microarray, Cell cycle, Ionizing radiation, Human fibroblasts, EPIG

2007-08-01 | GSE7075 | 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