Linking single-cell measurements of mass, growth rate, and gene expression
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA498045 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8093940_1.fastq.gz | Fastqsanger.gz | |||
| SRR8093940_2.fastq.gz | Fastqsanger.gz | |||
| SRR8093950_1.fastq.gz | Fastqsanger.gz | |||
| SRR8093950_2.fastq.gz | Fastqsanger.gz | |||
| SRR8093960_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 1528 |
Similar Datasets
Project description:We introduce a microfluidic platform that enables single-cell mass and growth rate measurements upstream of single-cell RNA-sequencing (scRNA-seq) to generate paired single-cell biophysical and transcriptional data sets. Biophysical measurements are collected with a serial suspended microchannel resonator platform (sSMR) that utilizes automated fluidic state switching to load individual cells at fixed intervals, achieving a throughput of 120 cells per hour. Each single-cell is subsequently captured downstream for linked molecular analysis using an automated collection system. From linked measurements of a murine leukemia (L1210) and pro-B cell line (FL5.12), we identify gene expression signatures that correlate significantly with cell mass and growth rate. In particular, we find that both cell lines display a cell-cycle signature that correlates with cell mass, with early and late cell-cycle signatures significantly enriched amongst genes with negative and positive correlations with mass, respectively. FL5.12 cells also show a significant correlation between single-cell growth efficiency and a G1-S transition signature, providing additional transcriptional evidence for a phenomenon previously observed through biophysical measurements alone. Importantly, the throughput and speed of our platform allows for the characterization of phenotypes in dynamic cellular systems. As a proof-of principle, we apply our system to characterize activated murine CD8+ T cells and uncover two unique features of CD8+ T cells as they become proliferative in response to activation: i) the level of coordination between cell cycle gene expression and cell mass increases, and ii) translation-related gene expression increases and shows a correlation with single-cell growth efficiency. Overall, our approach provides a new means of characterizing the transcriptional mechanisms of normal and dysfunctional cellular mass and growth rate regulation across a range of biological contexts.
2018-10-26 | GSE121655 | GEO
Project description:Mass and growth rate are highly integrative measures of cell physiology not discernable via genomic measurements. Here, we introduce a microfluidic platform enabling direct measurement of single-cell mass and growth rate upstream of highly multiplexed single-cell profiling such as single-cell RNA sequencing. We resolve transcriptional signatures associated with single-cell mass and growth rate in L1210 and FL5.12 cell lines and activated CD8+ T cells. Further, we demonstrate a framework using these linked measurements to characterize biophysical heterogeneity in a patient-derived glioblastoma cell line with and without drug treatment. Our results highlight the value of coupled phenotypic metrics in guiding single-cell genomics.
| S-EPMC6260722 | biostudies-literature
Project description:miRNA expression profile is related to vestibular schwannoma growth rate
| PRJNA513253 | ENA
Project description:TAK1 is essential for growth and maintenance of skeletal muscle mass
| PRJNA413137 | ENA
Project description:Tumor miRNA expression is related to the growth rate of sporadic vestibular schwannomas. Rapid tumor growth is associated with deregulation of several miRNAs, including up-regulation of miR-29abc, miR-19, miR-340-5p, miR-21 and miR-221 and down-regulation of miR-744 and let-7b. Gene ontologies affected by the deregulated miRNAs included neuron development and differentiation, gene silencing and negative regulation of various biological processes, including cellular and intracellular signalling and metabolism. We used microarray to determine the miRNA expresison in vestibular schwannoma their relation to the growth rate.
2019-01-08 | GSE124717 | GEO
Project description:We studied the relation between growth rate and genomewide gene expression, cell cycle progression, and glucose metabolism in 36 steady state continuous cultures limited by one of six different nutrients (glucose, ammonium, sulfate, phosphate, uracil or leucine). The expression of more than a quarter of all yeast genes is linearly correlated with growth rate, independently of the limiting nutrient. The subset of negatively growth-correlated genes is most enriched for peroxisomal functions, whereas positively correlated genes mainly encode ribosomal functions. Many (not all) genes associated with stress response are strongly correlated with growth rate, as are genes that are periodically expressed under conditions of metabolic cycling. We confirmed a linear relationship between growth rate and the fraction of the cell population in the G0/G1 cell cycle phase, independent of limiting nutrient. Cultures limited by auxotrophic requirements wasted excess glucose, whereas those limited on phosphate, sulfate or ammonia did not; this phenomenon (reminiscent of the "Warburg effect" in cancer cells) was confirmed in batch cultures. Using an aggregate of gene expression values, we predict (in both continuous and batch cultures) an "instantaneous growth rate". This concept is useful in interpreting the systemlevel connections among growth rate, metabolism, stress and the cell cycle. Keywords: growth condition design
2007-08-21 | GSE8825 | GEO
Project description:RNA-Seq of Corynebacterium glutamicum ATCC13032 differing in growth rates reveals the growth rate modulon
| PRJEB30012 | ENA
Project description:Cellular resources are limited and their relative allocation to gene expression programmes determines physiological states and global properties such as the growth rate. Quantitative studies using various growth conditions have singled out growth rate as a major physiological variable explaining relative protein abundances. Here, we used the simple eukaryote Schizosaccharomyces pombe to determine the importance of growth rate in explaining relative changes in protein and mRNA levels during growth on a series of non-limiting nitrogen sources. Although half of fission yeast genes were significantly correlated with the growth rate, this came alongside widespread nutrient-specific regulation. Proteome and transcriptome often showed coordinated regulation but with notable exceptions, such as metabolic enzymes. Genes positively correlated with growth rate participated in every level of protein production with the notable exception of RNA polymerase II, whereas those negatively correlated mainly belonged to the environmental stress response programme. Critically, metabolic enzymes, which represent ~55-70% of the proteome by mass, showed mainly condition-specific regulation. Specifically, many enzymes involved in glycolysis and NAD-dependent metabolism as well as the fermentative and respiratory pathways were condition-dependent and not consistently correlated with growth. In summary, we provide a rich account of resource allocation to gene expression in a simple eukaryote, advancing our basic understanding of the interplay between growth-rate dependent and nutrient-specific gene expression.
2022-02-24 | PXD027835 | Pride
Project description:Gene expression measured at maximal Salmonella growth rate in different media Keywords: other
2006-03-04 | GSE2456 | GEO
Project description:The B. subtilis transcriptome was analyzed under conditions of different growth rates, i.e. during growth in different cultivation media. Gene-level intensities were scaled based on the intensity values of 10 spike-in transcripts. This approach allowed to determine the total mRNA fraction out of the total RNA pool. The data revealed that the proportion of total mRNA in total RNA remained constant across samples which implies that total mRNA abundance in B. subtilis increases proportionally to the growth rate.
2016-04-18 | GSE78108 | GEO