Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Drop-seq analysis of wild-type (TLAB) zebrafish embryos from high to 6-somite stage (12 timepoints)

ABSTRACT: Wild-type zebrafish embryos were mechanically dissociated and profiled using Drop-seq

ORGANISM(S): Danio rerio

PROVIDER: GSE106474 | GEO | 2018/04/27

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

10x analysis of wild-type (TLAB) and MZoep zebrafish embryos at 6-somite stage

Project description:Wild-type and MZoep zebrafish embryos were mechanically dissociated and profiled using 10x Genomics pipeline.

2018-04-27 | GSE112824 | GEO

Drop-seq analysis of wild-type (TLAB) zebrafish embryos from high to 6-somite stage (12 timepoints)

Project description:Drop-seq analysis of wild-type (TLAB) zebrafish embryos from high to 6-somite stage (12 timepoints)

| PRJNA417290 | ENA

Integrin a5, aV, and aVb3 in zebrafish embryos at the 12 somite stage

Project description:Integrins are a major class of heterodimeric adhesion receptors composed of an a and b subunit that mediate cell adhesion to the extracellular matrix (ECM). The extracellular matrix protein fibronectin is important for early vertebrate development, and Integrin a5b1 and aVb3 are the two primary fibronectin receptors. To better define the integrin – ECM protein network at 10-13 somite stage of zebrafish development, we performed co-immunoprecipitation and Mass Spectrometry (MS) based proteomics using FLAG-tagged Integrin a5, aV, and aVb3 expressed in maternal zygotic a5 mutant (MZa5-/-) embryos. We found that Integrin a5b1 and aVb1 are the functional fibronectin receptors, whereas Integrin aVb3 displayed low affinity to both fibronectins (Fn1a and Fn1b). In addition, basement membrane ligands Laminins (lama1, lamb1a, lamc1) are roughly equal in all three datasets while Thrombospondins (thbs3b, thbs4b) and cartilage oligomeric matrix protein (comp/thbs5) are found exclusively in the aV dataset. Our results suggest a diverse role of aV class integrins in ECM protein recruitment.

2021-09-10 | PXD024665 | Pride

Drop-seq analysis of bleomycin-treated and control mouse lung single-cell suspensions

Project description:Cell suspensions were prepared from mouse lungs dissociated at baseline or 14 days after intratracheal bleomycin injury, and single cell mRNA-seq libraries were generated with Drop-seq.

2018-10-25 | E-MTAB-7142 | biostudies-arrayexpress

Drop-seq analysis of bleomycin-treated and control mouse lung single-cell suspensions

2018-10-24 | GSE111664 | GEO

Size-reduced embryos reveal a gradient scaling-based mechanism for zebrafish somite formation.

Project description:Little is known about how the sizes of animal tissues are controlled. A prominent example is somite size, which varies widely both within an individual and across species. Despite intense study of the segmentation clock governing the timing of somite generation, how it relates to somite size is poorly understood. Here, we examine somite scaling and find that somite size at specification scales with the length of the presomitic mesoderm (PSM) despite considerable variation in PSM length across developmental stages and in surgically size-reduced embryos. Measurement of clock period, axis elongation speed and clock gene expression patterns demonstrate that existing models fail to explain scaling. We posit a 'clock and scaled gradient' model, in which somite boundaries are set by a dynamically scaling signaling gradient across the PSM. Our model not only explains existing data, but also makes a unique prediction that we confirm experimentally - the formation of periodic 'echoes' in somite size following perturbation of the size of one somite. Our findings demonstrate that gradient scaling plays a central role in both progression and size control of somitogenesis.

| S-EPMC6031319 | biostudies-literature

Zebrafish periderm at 4-somite stage

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-01-13 | GSE140241 | GEO

Single cell RNA sequencing of cells isolated from the intestinal crypts of mice bearing epithelial cell-specific Ptger4 ablation (Drop-seq)

Project description:Crypts isolated from the small intestine of mice bearing epithelial cell-specific ablation of the Ptger4 gene (VillinCrePtger4flox, "V") and normal littermate control mice (Ptger4flox, "F") were dissociated into single cell suspensions and subjected to the Drop-seq protocol. N = 2 mice per genotype were independently processed as biological replicates (V1, V2 and F1, F2). A total of three Drop-seq collections (samples) were processed for each genotype, two from the first biological replicate (V1A, V1B, F1A, F1B) and one from the second biological replicate (V2, F2).

2019-12-21 | GSE142418 | GEO

Sequencing of smallRNAs of fish embryos in somite stage

Project description:Sequencing of smallRNA of different Nothobranchius furzeri (Nfu) strains and 8 further anual and not anual fish species for investigation of its differential expression with and without diapause.

2019-05-09 | GSE81231 | GEO

Constraints on somite formation in developing embryos.

Project description:Segment formation in vertebrate embryos is a stunning example of biological self-organization. Here, we present an idealized framework, in which we treat the presomitic mesoderm (PSM) as a one-dimensional line of oscillators. We use the framework to derive constraints that connect the size of somites, and the timing of their formation, to the growth of the PSM and the gradient of the somitogenesis clock period across the PSM. Our analysis recapitulates the observations made recently in ex vivo cultures of mouse PSM cells, and makes predictions for how perturbations, such as increased Wnt levels, would alter somite widths. Finally, our analysis makes testable predictions for the shape of the phase profile and somite widths at different stages of PSM growth. In particular, we show that the phase profile is robustly concave when the PSM length is steady and slightly convex in an important special case when it is decreasing exponentially. In both cases, the phase profile scales with the PSM length; in the latter case, it scales dynamically. This has important consequences for the velocity of the waves that traverse the PSM and trigger somite formation, as well as the effect of errors in phase measurement on somite widths.

| S-EPMC6769302 | biostudies-literature

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