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Items: 1 to 20 of 3545

1.

Developmental and Injury-induced Changes in DNA Methylation in Regenerative versus Non-regenerative Regions of the Vertebrate (Xenopus laevis) Central Nervous System

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Xenopus laevis
Type:
Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms:
GPL20998 GPL21248
97 Samples
Download data: BW
Series
Accession:
GSE183357
ID:
200183357
2.

Developmental and Injury-induced Changes in DNA Methylation in Regenerative versus Non-regenerative Regions of the Vertebrate (Xenopus laevis) Central Nervous System Characterized by Whole Genome Bisulfite Sequencing (WGBS)

(Submitter supplied) Xenopus is uniquely suited for identifying core features of successful CNS axon regeneration, because parts of its CNS (e.g., eye), regenerate axons throughout life, whereas others (e.g., hindbrain) do so only as tadpoles. We performed bisulfite whole genome bisulfite methylation sequencing (WGBS) on juvenile frog eye after optic nerve injury, and on hindbrain samples from tadpole and juvenile frog after spinal cord injury during the peak phase of axon regeneration, to compare tissue-related and injury-induced differences in DNA methylation among them.
Organism:
Xenopus laevis
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL20998
21 Samples
Download data: BW
Series
Accession:
GSE183355
ID:
200183355
3.

Developmental and Injury-induced Changes in DNA Methylation in Regenerative versus Non-regenerative Regions of the Vertebrate (Xenopus laevis) Central Nervous System assayed by 5hmC MeDIP and by ChIP-seq for Histone Markers

(Submitter supplied) Xenopus is uniquely suited for identifying core features of successful CNS axon regeneration, because parts of its CNS (e.g., eye), regenerate axons throughout life, whereas others (e.g., hindbrain) do so only as tadpoles. To aid in the interpretation of bisulfite whole genome methylation sequencing (WGBS) on juvenile frog eye after optic nerve injury, and on hindbrain samples from tadpole and juvenile frog after spinal cord injury during the peak phase of axon regeneration, we performed ChIP-seq for histone modifications associated with active gene expression (H3K4me3 & H3K27ac) and repressed gene expression (H3K27me3 & H3K9me3) on these same tissues, as well as DNA-immunoprecipitation sequencing (DIP seq) for 5-hydroxymethyl cytosine (5hmC) on eye samples during optic nerve regeneration.
Organism:
Xenopus laevis
Type:
Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform:
GPL21248
76 Samples
Download data: BW
Series
Accession:
GSE183350
ID:
200183350
4.

High expression profiling analysis of the early response to spinal cord injury identified a key role for mTORC1 signaling

(Submitter supplied) Xenopus laevis are able to regenerate the spinal cord during larvae stages through the activation of neural stem progenitor cells (NSPC). Here, we use high-resolution expression profiling to characterize the early transcriptome changes induced after spinal cord injury, and identify the signals that trigger NSPC proliferation. The analysis delineates a pathway that starts with a rapid and transitory activation of immediate early genes, followed by migration processes and immune response genes, the pervasive increase of NSPC specific ribosome biogenesis factors, and genes involved in stem cell proliferation. more...
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL22393 GPL17682
111 Samples
Download data: TXT
Series
Accession:
GSE165343
ID:
200165343
5.

Asymmetric robustness in the feedback control of the retinoic acid network response to environmental disturbances

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Xenopus laevis
Type:
Expression profiling by RT-PCR; Expression profiling by high throughput sequencing
Platforms:
GPL28865 GPL22393
168 Samples
Download data
Series
Accession:
GSE154408
ID:
200154408
6.

Robustness in the feedback control of the retinoic acid network response to environmental disturbances (BioMark-qRT-PCR)

(Submitter supplied) Retinoic acid (RA) is a central developmental signal whose perturbation results in teratogenic outcomes. RA is tightly regulated during early embryonic development to achieve fine-tuning of the instructive and permissive signals regulating multiple developmental processes including head formation. We aim to identify the key mechanisms underlying the homeostatic regulation and tuning of the retinoic acid signaling levels, the disruption of which in the head lead to wide ranging developmental malformations including microcephaly and other craniofacial defects. more...
Organism:
Xenopus laevis
Type:
Expression profiling by RT-PCR
Platform:
GPL28865
72 Samples
Download data: XLSX
Series
Accession:
GSE154407
ID:
200154407
7.

Robustness of retinoic acid regulatory homeostasis during early development (RNA-seq)

(Submitter supplied) Retinoic acid (RA) is a central developmental signal whose perturbation results in teratogenic outcomes. RA are tightly regulated during early embryonic development to achieve fine-tuning of the instructive and permissive signals regulating multiple developmental processes including head formation. We aim to identify the key mechanisms underlying the homeostatic regulation and tuning of the retinoic acid signaling levels, the disruption of which in the head lead to wide ranging developmental malformations including microcephaly and other craniofacial defects. more...
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL22393
96 Samples
Download data: TXT
Series
Accession:
GSE154399
ID:
200154399
8.

Single-cell transcriptomic analysis reveals unique cell types and patterns of gene expression in the frog corneal epithelium.

(Submitter supplied) Here, we use scRNA-seq to expand our understanding of the vertebrate corneal epithelium in an amphibian model, having undertaken a comprehensive characterization of cellular and transcriptional heterogeneity to identify novel corneal marker genes.
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL28901
1 Sample
Download data: MTX, TSV
Series
Accession:
GSE154896
ID:
200154896
9.

The molecular basis of coupling between poly(A)-tail length and translational efficiency

(Submitter supplied) In animal oocytes and early embryos, mRNA poly(A)-tail length strongly influences translational efficiency (TE), but later in development this coupling between tail length and TE disappears. Here, we elucidate how this coupling is first established and why it disappears. Overexpressing cytoplasmic poly(A)-binding protein (PABPC) in frog oocytes specifically improved translation of short-tailed mRNAs, thereby diminishing coupling between tail length and TE. more...
Organism:
Mus musculus; Homo sapiens; Xenopus laevis
Type:
Expression profiling by high throughput sequencing; Other
Platforms:
GPL16791 GPL17021 GPL18936
79 Samples
Download data: TXT
10.

Linker histone H1.8 inhibits chromatin-binding of condensins and DNA topoisomerase II to tune chromosome compaction and individualization

(Submitter supplied) Hi-C on reconstituted mitotic chromosomes in Xenopus system in IGG or specific depleted egg extracts to study to role of condensin and linker histone in chromosome condensation
Organism:
Xenopus laevis
Type:
Other
Platform:
GPL22393
25 Samples
Download data: MCOOL
11.

Comprehensive expression profile reveals dynamic changes in Xenopus gene expression depending on the duration of activin A treatment.

(Submitter supplied) In amphibian embryo, the animal cap explants treated with activin A, which is a member of TGF-β family protein, have a potent of Spemann-Mangold organizer-like activities, leading the induction of mesendodermal tissue. We report the temporal RNA expression profile of the mesendodermal cell lineage induced by activin A to Xenopus animal cap explants, which have multipotency. Depending on the duration of activin A treatment to animal cap, dynamic changes of gene expressions were observed. more...
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21248
15 Samples
Download data: XLSX
Series
Accession:
GSE153925
ID:
200153925
12.

Fibroblast Dedifferentiation as a Determinant of Successful Regeneration

(Submitter supplied) Limb regeneration, while observed lifelong in salamanders, is restricted to pre-metamorphic stages in Xenopus laevis frogs. After amputation, post-metamorphic frogs form a blastema that grows only an unsegmented cartilage rod. Whether this loss is due to systemic factors such as the immune system or due to an intrinsic incapability of cells to form competent stem cells has been unclear. Here, we use genetic fate mapping to establish that, as in axolotl, connective tissue (CT) cells form the post-metamorphic frog blastema. more...
Organism:
Xenopus laevis; Ambystoma mexicanum
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL27159 GPL22800 GPL28901
18 Samples
Download data: MTX, TSV
Series
Accession:
GSE165901
ID:
200165901
13.

Poly(I:C) transfection time course in Xenopus laevis A6 cells

(Submitter supplied) This study was designed to identify Xenopus laevis genes that respond to stimulation with an immune agonist, poly(I:C).
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL28901
12 Samples
Download data: TXT
Series
Accession:
GSE166455
ID:
200166455
14.

3D genomics across the tree of life reveals condensin II as a determinant of architecture type

(Submitter supplied) We investigated genome folding across the eukaryotic tree of life. We find four general manifestations of genome organization at chromosome-scale that each emerge and disappear repeatedly over the course of evolution. The submission represents chromosome-length Hi-C contact maps, architecture type and homolog separation analyses for 26 species across the tree of life, representing all subphyla of chordates, all 7 extant vertebrate classes, and 7 out of 9 major animal phyla, as well as plants and fungi.
Organism:
Saccharomyces cerevisiae; Drosophila melanogaster; Gallus gallus; Hypsibius dujardini; Lethenteron camtschaticum; Strongylocentrotus purpuratus; Ciona intestinalis; Pleurobrachia bachei; Acropora millepora; Python bivittatus; Triticum aestivum; Caenorhabditis elegans; Aplysia californica; Aedes aegypti; Culex quinquefasciatus; Homo sapiens; Muntiacus reevesi; Muntiacus muntjak; Arachis hypogaea; Agaricus bisporus; Branchiostoma lanceolatum; Xenopus laevis; Notamacropus eugenii; Pygocentrus nattereri; Cristatella mucedo; Clonorchis sinensis; Chiloscyllium punctatum
Type:
Other
30 related Platforms
32 Samples
Download data: BEDPE, FASTA, HIC, VCF, WIG
Series
Accession:
GSE169088
ID:
200169088
15.

Induction of dorsal mesodermal genes by pinhead and chordin

(Submitter supplied) Xenopus embryonic ectodermal cells are responsive to various inducing factors. Mesoderm is specified and patterned by extracellular factors including FGF, Nodal, BMP and Wnt families. Pinhead is another secreted protein implicated in mesoderm formation. We found that Pinhead physically interacts with and antagonizes ADMP (anti-dorsalizing morphogenetic protein) that acts as BMP-like protein to promote ventral mesoderm formation. more...
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17682
8 Samples
Download data: XLSX
Series
Accession:
GSE168370
ID:
200168370
16.

Identification of the FTO-FOXJ1 axis as a conserved regulatory module of embryonic and homeostatic motile ciliogenesis

(Submitter supplied) Adenosine N6-methylation (m6A) is one of the most pervasive mRNA modifications, and yet the physiological significance of m6A removal (demethylation) remains elusive. Here we report the m6A demethylase FTO functions as a conserved regulator of motile ciliogenesis. Mechanistically, FTO demethylates and thereby stabilizes the mRNA encoding the master ciliary transcription factor FOXJ1. Depletion of Fto in Xenopus laevis embryos caused widespread motile cilia defects, and Foxj1 was identified as one of the major phenocritical targets. more...
Organism:
Xenopus laevis
Type:
Other
Platform:
GPL22426
4 Samples
Download data: TXT
Series
Accession:
GSE167139
ID:
200167139
17.

Anterior-Posterior Rotation Transcriptome RNA-Sequencing Analysis of X. laevis

(Submitter supplied) To analyze the limits of embryo robustness, several different types of surgeries were performed on the anterior-posterior neural axis of Xenopus laevis embryos. Our RNA-Seq data suggests a model in which aspects of early neural plasticity are associated with unique pathways and their associated genes. The transcriptome analysis reveals several combinations of pathways and genes that incorporate and heal foreign tissue, but also re-pattern the anterior-posterior axis. more...
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL29672
74 Samples
Download data: TXT
Series
Accession:
GSE165763
ID:
200165763
18.

Cellular response to spinal cord injury in regenerative and non-regenerative stages in Xenopus laevis.

(Submitter supplied) Background: The efficient regenerative abilities at larvae stages followed by a non-regenerative response after metamorphosis in froglets makes Xenopus an ideal model organism to understand the cellular responses leading to spinal cord regeneration. Methods: We compared the cellular response to spinal cord injury between the regenerative and non-regenerative stages of Xenopus laevis. For this analysis, we used electron microscopy, immunofluorescence and histological staining of the extracellular matrix. more...
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL22393
2 Samples
Download data: TXT
Series
Accession:
GSE164204
ID:
200164204
19.

Proteomic and Transcriptomic Analysis of Neural Cell Fate in Developing Xenopus laevis Embryos and Explants

(Submitter supplied) Purpose: Study the developing neural cell fate of the D1 blastomere in the 8-cell embryo. Determine what transcripts are dependant on cell/cell signaling and which are inherit to the single cell and do not depend on the rest of the embryo. Methods: D1 blastomere was either injected with fluorescent dye or explanted away from the developing embryo. Transcript profile was taken at 7 time points: 8-cell, 16-cell, 32-cell, blastula, gastrula, early neurula, and mid/late neurula. more...
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21248
42 Samples
Download data: TXT
Series
Accession:
GSE147621
ID:
200147621
20.

Alpha-tocopherol exerts protective function against the mucotoxicity of particulate matter in amphibian and human goblet cells

(Submitter supplied) Exposure to particulate matter (PM) in ambient air is known to increase the risk of cardiovascular disorders and mortality. The cytotoxicity of PM is mainly due to the abnormal increase of reactive oxygen species (ROS), which damage cellular components such as DNA, RNA, and proteins. The correlation between PM exposure and human disorders, including mortality, is based on long-term exposure. In this study we have investigated acute responses of mucus-secreting goblet cells upon exposure to PM derived from a heavy diesel engine. more...
Organism:
Xenopus laevis; Bombina orientalis
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL26992 GPL18936
16 Samples
Download data: FA, ZIP
Series
Accession:
GSE163875
ID:
200163875
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