Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The transcriptome dynamics of single cells during the cell cycle.

ABSTRACT: The transcriptome dynamics of single cells during the cell cycle.

PROVIDER: PRJNA596453 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10733630_1.fastq.gz	Fastqsanger.gz
	SRR10733630_2.fastq.gz	Fastqsanger.gz
	SRR10733631_1.fastq.gz	Fastqsanger.gz
	SRR10733631_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

The transcriptome dynamics of single cells during the cell cycle.

Project description:We used the dataset to perform in-silico sorting of single cell transcriptomes along the cell cycle and thus being able to investigate gene expression dynamics along the mammalian cell cycle.

2020-11-19 | GSE142277 | GEO

Single-cell profiling reveals transcriptome dynamics during bovine oocyte growth

Project description:Single-cell profiling reveals transcriptome dynamics during bovine oocyte growth

| PRJNA1049029 | ENA

The transcriptome dynamics of single cells during the cell cycle.

Project description:The cell cycle is among the most basic phenomena in biology. Despite advances in single-cell analysis, dynamics and topology of the cell cycle in high-dimensional gene expression space remain largely unknown. We developed a linear analysis of transcriptome data which reveals that cells move along a planar circular trajectory in transcriptome space during the cycle. Non-cycling gene expression adds a third dimension causing helical motion on a cylinder. We find in immortalized cell lines that cell cycle transcriptome dynamics occur largely independently from other cellular processes. We offer a simple method ("Revelio") to order unsynchronized cells in time. Precise removal of cell cycle effects from the data becomes a straightforward operation. The shape of the trajectory implies that each gene is upregulated only once during the cycle, and only two dynamic components represented by groups of genes drive transcriptome dynamics. It indicates that the cell cycle has evolved to minimize changes of transcriptional activity and the related regulatory effort. This design principle of the cell cycle may be of relevance to many other cellular differentiation processes.

| S-EPMC7672610 | biostudies-literature

Nucleosome plasticity during the cell cycle

Project description:Nucleosome organization and dynamics play a central role in controlling the DNA accessibility to regulatory factors of many critical cellular functions, especially gene regulation. However, despite extensive studies, the main factors determining nucleosome positioning and its fluctuation during cell cycle still remain elusive. Here, we present a large-scale study of nucleosome plasticity throughout the cell cycle and its interplay with gene expression based on genome-wide nucleosome positioning and mRNA abundance. We have clusterized distinct nucleosome architectures around transcription start sites and replication origins and studied their dynamics during the cell cycle progression. The most significant cell cycle-dependent changes occur at G1-S and G2-M transitions due to a large changes in gene expression in cell cycle regulatory genes. Taken together, our accurate study provides a dynamic picture of chromatin organization along cell cycle and its interplay with gene expression.

2014-10-09 | E-MTAB-2839 | biostudies-arrayexpress

Cell cycle dynamics of chromosomal organisation at single-cell resolution

Project description:Chromosomes in proliferating metazoan cells undergo dramatic structural metamorphoses every cell cycle, alternating between a highly condensed mitotic structure facilitating chromosome segregation, and a decondensed interphase structure accommodating transcription, gene silencing and DNA replication. These cyclical structural transformations have been evident under the microscope for over a century, but their molecular-level analysis is still lacking. Here we use single-cell Hi-C to study chromosome conformations in thousands of individual cells, and discover a continuum of cis-interaction profiles that finely position individual cells along the cell cycle. We show that chromosomal compartments, topological domains (TADs), contact insulation and long-range loops, all defined by ensemble Hi-C maps, are governed by distinct cell cycle dynamics. In particular, DNA replication correlates with build-up of compartments and reduction in TAD insulation, while loops are generally stable from G1 through S and G2. Analysing whole genome 3D structural models using haploid cell data, we discover a radial architecture of chromosomal compartments with distinct epigenomic signatures. Our single-cell data creates an essential new paradigm for the re-interpretation of chromosome conformation maps through the prism of the cell cycle.

2017-07-06 | GSE94489 | GEO

Single-cell 5-hydroxymethyl cytosine dynamics during remote memory formation

Project description:Single-cell 5-hydroxymethyl cytosine dynamics during remote memory formation

| PRJNA1070287 | ENA

Gene expression pattern of single mES cells during cell cycle stages

Project description:Gene expression pattern of single mES cells during cell cycle stages

| PRJEB6989 | ENA

Differential scaling between G1 protein production and cell size dynamics promotes commitment to the cell division cycle in budding yeast

Project description:In the unicellular eukaryote Saccharomyces cerevisiae, Cln3-CDK activity enables Start, the irreversible commitment to the cell division cycle. However, the concentration of Cln3 has been paradoxically considered to remain constant during G1, due to the presumed scaling of its production rate with cell size dynamics. Measuring metabolic and biosynthetic activity during cell cycle progression in single cells, we found that cells exhibit pulses in protein production rate, which do not scale with cell size dynamics, but -following the intrinsic metabolic dynamics- peak around Start. Using a viral-based bicistronic construct and targeted proteomics to measure Cln3 at the single-cell and population level, we show that the differential scaling between protein production and cell size leads to a temporal increase in Cln3 concentration, and passage through Start. This differential scaling causes Start in both daughter and mother cells, across growth conditions. Thus, uncoupling between two fundamental physiological parameters drives cell cycle commitment.

2019-10-29 | PXD015327 | Pride

Differential scaling between G1 protein production and cell size dynamics promotes commitment to the cell division cycle in budding yeast

Project description:In the unicellular eukaryote Saccharomyces cerevisiae, Cln3–cyclin-dependent kinase activity enables Start, the irreversible commitment to the cell division cycle. However, the concentration of Cln3 has been paradoxically considered to remain constant during G1, due to the presumed scaling of its production rate with cell size dynamics. Measuring metabolic and biosynthetic activity during cell cycle progression in single cells, we found that cells exhibit pulses in their protein production rate. Rather than scaling with cell size dynamics, these pulses follow the intrinsic metabolic dynamics, peaking around Start. Using a viral- based bicistronic construct and targeted proteomics to measure Cln3 at the single-cell and population levels, we show that the differential scaling between protein production and cell size leads to a temporal increase in Cln3 concentration, and passage through Start. This differential scaling causes Start in both daughter and mother cells across growth conditions. Thus, uncou- pling between two fundamental physiological parameters drives cell cycle commitment.

2022-05-16 | PXD029959 | Pride

Gene Regulation Dynamics during the Cell Cycle uncovered by RNA velocity and deep-learning

Project description:Gene Regulation Dynamics during the Cell Cycle uncovered by RNA velocity and deep-learning

| PRJNA705145 | ENA