Time-resolved assessment of single-cell protein secretion by sequencing
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA826085 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18735443_1.fastq.gz | Fastqsanger.gz | |||
| SRR18735443_2.fastq.gz | Fastqsanger.gz | |||
| SRR18735444_1.fastq.gz | Fastqsanger.gz | |||
| SRR18735444_2.fastq.gz | Fastqsanger.gz | |||
| SRR18735445_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 28 |
Similar Datasets
Project description:Secreted proteins play critical roles in cellular communication. Methods enabling concurrent measurement of cellular protein secretion, phenotypes and transcriptomes are still unavailable. Here, we describe Time-Resolved Assessment of Protein Secretion from single cells by sequencing (TRAPS-seq). Released proteins are trapped onto cell surface and probed by oligonucleotide-barcoded antibodies before simultaneously sequenced with transcriptomes in single cells. TRAPS-seq unravels the phenotypic and transcriptional determinants of the secretion of pleiotropic Th1 cytokines (IFN-γ, IL-2 and TNF-α) in activated T cells. We further demonstrate the use of TRAPS-seq to track dynamic secretion of multiple cytokines over time, uncovering unique molecular signatures that govern the preservation or transition of single-cell cytokine secretions. Our results revealed that early central memory T cells with CD45RA expression (TCMRA) are important in both the production and maintenance of polyfunctional cytokines. TRAPS-seq presents a unique tool for seamless integration of secretomics measurement with multi-omics profiling in single cells.
2023-01-11 | GSE200690 | GEO
Project description:Time-resolved transcript, protein and metabolite profiling of Arabidopsis roots in simulated microgravity
| PRJEB14621 | ENA
Project description:Protein-protein interactions play host to several cellular processes that depend heavily on both spatial and temporal regulation of these interactions. As such, understanding these parameters is necessary to fully comprehend and elucidate cellular processes and pathological disease states associated with them. Many advancements have allowed for more detailed characterization of these parameters, yet none are available to identify and quantify de novo protein-protein interactions with time-resolution at an organelle-wide scale. To address this, we have developed a quantitative mass-spectrometry method, time-resolved interactome profiling (TRIP). As a proof of concept, we utilize this methodology to elucidate alterations in interactions for the protein folding disease congenital hypothyroidism. We identify and deconvolute altered temporal engagement with pathways such as Hsp70/90 assisted folding, disulfide/redox processing, and N-glcosylation associated with hypothyroidism pathophysiology. We have coupled this methodology with functional siRNA screening and identified Vcp and Tex264 as key protein degradation components whose inhibition rescues mutant prohormone secretion. Ultimately, our results provide insight into the temporal coordination of protein homeostasis, and our TRIP method should find broad application in investigating other protein folding diseases and cellular processes.
2024-08-08 | PXD035681 | Pride
Project description:MicroRNAs are central regulators of the T cell function. We explored RNA expression profiles over the initial 24 h of human CD4+ T cell activation. We found high similarity in time-resolved miRNA expression courses comparing independent activations and different donors. The detected miRNA expression patterns could be grouped into six classes only, each with a defined time course. MiR-155-5p known for its role in T cell immunity showed the most prevalent expression changes, quantified with an hourly increase of about 60 molecules/cell. As demonstrated for miRNA-155-5p, the analysis of time-resolved miRNA and mRNA expression data allowed to increase the validation rate of predicted miRNA targets to close to 90 %. Combining our time-resolved expression analysis with an absolute quantification of miRNA expression changes, gives new insights into miRNA regulatory networks and indicates the functional dominance of specific miRNAs within the early T cell activation.
2020-09-04 | GSE136626 | GEO
Project description:MicroRNAs are central regulators of the T cell function. We explored RNA expression profiles over the initial 24 h of human CD4+ T cell activation. We found high similarity in time-resolved miRNA expression courses comparing independent activations and different donors. The detected miRNA expression patterns could be grouped into six classes only, each with a defined time course. MiR-155-5p known for its role in T cell immunity showed the most prevalent expression changes, quantified with an hourly increase of about 60 molecules/cell. As demonstrated for miRNA-155-5p, the analysis of time-resolved miRNA and mRNA expression data allowed to increase the validation rate of predicted miRNA targets to close to 90 %. Combining our time-resolved expression analysis with an absolute quantification of miRNA expression changes, gives new insights into miRNA regulatory networks and indicates the functional dominance of specific miRNAs within the early T cell activation.
2020-09-04 | GSE136625 | GEO
Project description:A time-resolved transcriptome atlas of maize grain development
| PRJNA666644 | ENA
Project description:We employed time-resolved microRNA expression analyses upon the activation of peripheral CD4+ T cells to track and functionally relate changes on cellular signaling in patients at different stages of PD
2023-01-23 | GSE202666 | GEO
Project description:We employed time-resolved RNA expression analyses upon the activation of peripheral CD4+ T cells to track and functionally relate changes on cellular signaling in patients at different stages of PD
2023-01-23 | GSE202665 | GEO
Project description:Protein secretion is an essential process in cell biology. The conventional secretion pathway is well known, and involves proteins with a signal sequence being directed into the endoplasmic reticulum. Once in the lumen of the endoplasmic reticulum, proteins are trafficked through the Golgi and remain separate from the cytosol throughout their journey to the outside of the cell. More recently, proteins without a signal sequence have been found outside the cell. These proteins are secreted unconventionally, and avoid the ER-Golgi route. For both pathways, some aspects remain unclear, particularly surrounding the regulation of protein secretion. Galectin-3, an unconventionally secreted protein, was used here to investigate both conventional and unconventional protein secretion. The unconventional protein secretion of galectin-3 is poorly understood. To address this, genetic manipulation of galectin-3 was used to gain insights into the mechanism of galectin-3 secretion. It was found that galectin-3 does not require unfolding or binding to cell surface glycoproteins to be secreted. Galectin-3 was also used to assess protein secretion using a genome-wide CRISPR screen. As galectin‑3 binds to cell surface glycoproteins, galectin-3 on the cell surface was used to assess secretion of these glycoproteins. Hits were validated by a glycoprotein secretion assay. Using this pipeline, 93 hits were identified as involved in protein secretion, of which 51 were novel hits not previously associated with protein secretion. Many of the hits identified also resulted in a phenotype of altered Golgi morphology, and five of these were investigated further. Two novel hits that localised to the Golgi were identified, TMEM220 and GPR161. GPR161 likely mediates its effect on Golgi morphology by its interaction with golgin A5. This thesis presents new insights into both conventional and unconventional protein secretion. Insights into the mechanism for galaectin-3 secretion were revealed. A novel Golgi-localised regulator of secretion, GRP161, was identified, with a mechanism for action suggested. Importantly, the list of 51 novel genes identified will serve as a useful resource for other researchers investigating protein secretion.
2020-09-13 | GSE157864 | GEO
Project description:UV laser-induced, time-resolved transcriptome resonses of Saccharomyces cerevisiae
| PRJNA530926 | ENA