Cellular population dynamics shape the route to human pluripotency
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA915944 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22892212.fastq.gz | Fastqsanger.gz | |||
| SRR22892213.fastq.gz | Fastqsanger.gz | |||
| SRR22892214.fastq.gz | Fastqsanger.gz | |||
| SRR22892215.fastq.gz | Fastqsanger.gz | |||
| SRR22892216.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 44 |
Similar Datasets
Project description:Human cellular reprogramming to induced pluripotency is still an inefficient process, which has hindered studying the role of critical intermediate stages. Here we take advantage of high efficiency reprogramming in microfluidics and temporal multi-omics to identify and resolve distinct sub-populations and their interactions. We perform secretome analysis and single-cell transcriptomics to show functional extrinsic pathways of protein communication between reprogramming sub-populations and the re-shaping of a permissive extracellular environment. We pinpoint the HGF/MET/STAT3 axis as a potent enhancer of reprogramming, which acts via HGF accumulation within the confined system of microfluidics, and in conventional dishes needs to be supplied exogenously to enhance efficiency. Our data suggest that human cellular reprogramming is a transcription factor-driven process that it is deeply dependent on extracellular context and cell population determinants.
| S-EPMC10192362 | biostudies-literature
Project description:Here we analyzed the gene expression dynamics of human cells reprogramming by using single cell RNA-seq (sc-RNAseq).
2023-01-31 | GSE221739 | GEO
Project description:Each TMT6 sample contains one replicate with the sub-samples representing subsequent time points. Detailed culture and processing methods are described in Panariello et al, Nat Comm, under revision.
2022-12-22 | MSV000090954 | MassIVE
Project description:Lima1 is an extensively studied prognostic marker of malignancy and is also considered to be a tumour suppressor, but its role in a developmental context of non-transformed cells is poorly understood. Here, we characterised the expression pattern and examined the function of Lima1 in mouse embryos and pluripotent stem cell lines. We found that Lima1 expression is controlled by the naïve pluripotency circuit and is required for the suppression of membrane blebbing. Moreover, Lima1 is essential for proper mitochondrial energetics, which is crucial for the growth of solid tumours. Forcing Lima1 expression enabled human pluripotent stem cells to be incorporated into murine pre-implantation embryos, trespassing the interspecies engraftment barrier. Thus, Lima1 is a key effector molecule that mediates the pluripotency control of membrane dynamics and cellular metabolism.
2021-12-16 | PXD025293 | Pride
Project description:Vaccination is one of the most efficient public healthcare measures to fight infectious diseases. Nevertheless, the immune mechanisms induced in vivo by vaccination are still unclear. The route of administration, an important vaccination parameter, can substantially modify the quality of the response. How the route of administration affects the generation and profile of immune responses is of major interest. Here, we aimed to extensively characterize the profiles of the innate and adaptive response to vaccination induced after intradermal, subcutaneous, or intramuscular administration with a modified vaccinia virus Ankara model vaccine in non-human primates. The adaptive response following subcutaneous immunization was clearly different from that following intradermal or intramuscular immunization. The subcutaneous route induced a higher level of neutralizing antibodies than the intradermal and intramuscular vaccination routes. In contrast, polyfunctional CD8+ T-cell responses were preferentially induced after intradermal or intramuscular injection. We observed the same dichotomy when analyzing the early molecular and cellular immune events, highlighting the recruitment of cell populations, such as CD8+ T lymphocytes and myeloid-derived suppressive cells, and the activation of key immunomodulatory gene pathways. These results demonstrate that the quality of the vaccine response induced by an attenuated vaccine is shaped by early and subtle modifications of the innate immune response. In this immunization context, the route of administration must be tailored to the desired type of protective immune response. This will be achieved through systems vaccinology and mathematical modeling, which will be critical for predicting the efficacy of the vaccination route for personalized medicine.
2021-05-17 | E-MTAB-10309 | biostudies-arrayexpress
Project description:Transcriptional profiles of rabbit skin infected via the intradermal or scarification route of infeciton assessing the early time post infection. Transcriptional profiles were assessed at 4hrs, 24hrs, and 48hrs post infection for each route of infection. Transcript variation is as compared to normal, uninfected rabbit skin.
2014-05-13 | GSE57564 | GEO
Project description:Transcriptional profiles of rabbit skin infected via the intradermal or scarification route of infeciton assessing the early time post infection. Transcriptional profiles were assessed at 4hrs, 24hrs, and 48hrs post infection for each route of infection. Transcript variation is as compared to normal, uninfected rabbit skin. Two condition, three time points per condition. 3 biological replicates per time point per condition. Normal rabbit skin was used as the control.
2014-05-13 | E-GEOD-57564 | biostudies-arrayexpress
Project description:Pluripotency is highly dynamic and progresses through a continuum of pluripotent stem-cell states. The two states that bookend the pluripotency continuum, naïve and primed, are well characterized, but our understanding of the intermediate states and transitions between them remain incomplete. Here, we dissect the dynamics of pluripotent state transitions underlying pre- to post-implantation epiblast differentiation. Through comprehensive mapping of the proteome, phosphoproteome, transcriptome, and epigenome of embryonic stem cells transitioning from naïve to primed pluripotency, we find that rapid, acute, and widespread changes to the phosphoproteome precede ordered changes to the epigenome, transcriptome, and proteome. Reconstruction of kinase-substrate networks reveals signaling cascades, dynamics, and crosstalk. Distinct waves of global proteomic changes mark discrete phases of pluripotency, with cell state-specific surface markers tracking pluripotent state transitions. Our data provide new insights into the multi-layered control of the phased progression of pluripotency and a foundation for modeling mechanisms regulating pluripotent state transitions (www.stemcellatlasorg).
2019-05-07 | PXD010621 | Pride
Project description:The shape of a cell within tissues can represent the history of chemical and physical signals that it encounters, but can information from cell shape regulate cellular phenotype independently? Using optimal control theory to constrain reaction-diffusion schemes that are dependent on different surface-to-volume relationships, we find that information from cell shape can be resolved from mechanical signals. We used microfabricated 3-D biomimetic chips to validate predictions that shape-sensing occurs in a tension-independent manner through β3 integrin signaling pathway in human kidney podocytes and smooth muscle cells. Differential proteomics and functional ablation assays indicate that β3 integrin is critical in transduction of shape signals through ezrin-radixin-moesin (ERM) family. We used experimentally determined diffusion coefficients and experimentally validated simulations to show that shape sensing is an emergent cellular property enabled by multiple molecular characteristics of β3 integrin. We conclude that 3-D cell shape information, transduced through tension-independent mechanisms, can regulate phenotype.
2018-07-26 | PXD008150 | Pride