Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Dissecting the Individual and Collective Regenerative Behavior of Muscle Stem Cells During Aging

ABSTRACT: Dissecting the Individual and Collective Regenerative Behavior of Muscle Stem Cells During Aging

PROVIDER: PRJNA497842 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Dissecting the Individual and Collective Regenerative Behavior of Muscle Stem Cells During Aging

Project description:We utilize an integrative genomics approach (bulk RNA-Seq, ATAC-Seq) to show how Muscle Stem Cells (MuSCs) from distinct age groups (young and aged) are significantly altered during the regenerative response. Transcriptional landscapes during quiescence, activation, proliferation and differentiation from young and aged mice are profiled and chromatin accessibility is compared.

2019-08-30 | GSE121589 | GEO

Triple negative breast tumors contain heterogeneous cancer cells expressing distinct KRAS-dependent collective and disseminative invasion programs

Project description:Inter-patient and intra-tumoral heterogeneity complicate the identification of predictive biomarkers and effective treatments for basal triple negative breast cancer (b-TNBC). Invasion is the initiating event in metastasis and can occur by both collective and single-cell mechanisms. We cultured primary organoids from a b-TNBC genetically engineered mouse model in 3D collagen gels to characterize their invasive behavior. We observed that organoids from the same tumor presented different phenotypes that we classified as non-invasive, collective and disseminative. To identify molecular regulators driving these invasive phenotypes, we developed a workflow to isolate individual organoids from the collagen gels based on invasive morphology and perform RNA sequencing. We next tested the requirement of differentially regulated genes for invasion using shRNA knock-down. Strikingly, KRAS was required for both collective and disseminative phenotypes. We then performed a drug screen targeting signaling nodes upstream and downstream of KRAS. We found that inhibition of EGFR, MAPK/ERK, or PI3K/AKT signaling reduced invasion. Of these, ERK inhibition was striking for its ability to potently inhibit collective invasion and dissemination. We conclude that different cancer cells in the same b-TNBC tumor can express different metastatic molecular programs and identified KRAS and ERK as essential regulators of collective and single cell dissemination.

2023-01-03 | GSE215069 | GEO

Inferring individual rules from collective behavior.

Project description: Not available

| S-EPMC2906562 | biostudies-literature

Individual learning phenotypes drive collective behavior.

Project description: Not available

| S-EPMC7395545 | biostudies-literature

Sox2-dependent fibronectin fibrillogenesis controls directional collective migration of Schwann cells

Project description:The extracellular matrix is essential for tissue formation and regeneration through the control of cellular behavior. Deregulation of extracellular matrix components is associated to disease, including neurodegeneration. After peripheral nerve injury, Schwann cells guide regrowing axons to their targets. These glial cells migrate collectively and provide an extracellular environment to enable neural repair. How this occurs remains poorly understood. Here, we show that Sox2 controls fibronectin fibrillogenesis in Schwann cells to provide a highly oriented extracellular matrix, which supports their rapid collective migration with a continuous cellular flow. Sox2 directly activates fibronectin expression in Schwann cells, leading to an increase in fibrillogenesis and cellular huddling. Accordingly, loss of fibrillogenesis leads to glial disassembly and disorganized axon regrowth. In vivo, 7 days post nerve injury, we found that pro-regenerative Schwann cells co-express Sox2 and the EIIIA-containing fibronectin splicing isoform. This mechanism is conserved in mammals, including humans, but absent in zebrafish. Taken together, our results demonstrate that Sox2 directly controls fibrillogenesis and provide a novel mechanism for the modification of the environmental architecture by glial cells during neuronal repair.

2020-02-11 | GSE94590 | GEO

Dissecting Collective Cell Behavior in Polarization and Alignment on Micropatterned Substrates.

Project description: Not available

| S-EPMC4571026 | biostudies-literature

Probabilistic models of individual and collective animal behavior.

Project description: Not available

| S-EPMC5841767 | biostudies-literature

Individual variation in preference behavior in sailfin fish refines the neurotranscriptomic pathway for mate preference

Project description:Social interactions can drive distinct gene expression profiles which may vary by social context. Here we use female sailfin molly fish (Poecilia latipinna) to identify genomic profiles associated with preference behavior in distinct social contexts: male-interactions (mate choice) versus female-interactions (shoaling partner preference). We measured behavior of 15 females interacting in a non-contact environment with either two males or two females for 30 minutes followed by whole brain transcriptomic profiling by RNA sequencing. We profiled females that exhibited high levels of social affiliation and great variation in preference behavior to identify an order of magnitude more differentially expressed genes associated with behavioral variation than by differences in social context. Using linear modeling (limma), we took advantage of the individual variation in preference behavior to identify unique gene sets that exhibited distinct correlational patterns of expression with preference behavior in each social context. By combining limma and weighted gene co-expression network analyses (WGCNA) approaches we identify a refined set of 401 genes robustly associated with mate preference that is independent of shoaling partner preference or general social affiliation. While our refined gene set confirmed neural plasticity pathways involved in moderating female preference behavior, we also identified a significant proportion of discovered that our preference-associated genes were enriched for ‘immune system’ gene ontology categories. We hypothesize that the association between mate preference and transcriptomic immune function is driven by the less well-known role of these genes in neural plasticity which is likely involved in higher-order learning and processing during mate choice decisions.

2023-07-01 | GSE233523 | GEO

Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics

Project description:This SuperSeries is composed of the following subset Series: GSE30537: Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics [mRNA profiling] GSE30538: Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics [ChIP-seq] Refer to individual Series

2011-10-10 | E-GEOD-30539 | biostudies-arrayexpress

Individual bee brain behavior-age

Project description:This experiment examines gene expression profiles in individual honey bee brains (adult worker Apis mellifera). The purpose is to test whether behavioral phenotype can be predicted by expression profiles in individual brains in a naturalistic context (i.e., colonies in the field). The two behavioral phenotypes examined are 'nurse' and 'forager'. Other factors examined are age, genotype (full-sister group), and colony environment.<br><br> An additional processed data file is available on the FTP site for this experiment.

2011-02-03 | E-MEXP-24 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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