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Items: 1 to 20 of 17312

1.

Interactions between genistein and Wnt pathway in colon adenocarcinoma and early embryos

(Submitter supplied) The Wnt signaling pathway is one of the most ancient and pivotal signaling cascades, governing diverse processes in development and cancer regulation. Within the realm of cancer treatment, genistein emerges as a promising candidate due to its multifaceted modulation of various signaling pathways, including the Wnt pathway. Despite promising preclinical studies, the precise mechanisms underlying genistein's therapeutic effects via Wnt modulation remain elusive. more...
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL34551
12 Samples
Download data: TXT
Series
Accession:
GSE268980
ID:
200268980
2.

Macrophages modulate fibrosis during newt lens regeneration.

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Pleurodeles waltl; Notophthalmus viridescens
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL32588 GPL32009
21 Samples
Download data
Series
Accession:
GSE236908
ID:
200236908
3.

Macrophages modulate fibrosis during newt lens regeneration [Nvir]

(Submitter supplied) Previous studies indicated that macrophages play a role during lens regeneration in newts, but their function has not been tested experimentally. Here we generated a transgenic newt reporter line in which macrophages can be visualized in vivo. Using this new tool, we analyzed the location of macrophages during lens regeneration. We uncovered early gene expression changes using bulk RNAseq in two newt species, Notophthalmus viridescens and Pleurodeles waltl. more...
Organism:
Notophthalmus viridescens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32588
12 Samples
Download data: CSV, FASTA
Series
Accession:
GSE236907
ID:
200236907
4.

Macrophages modulate fibrosis during newt lens regeneration [PWaltl]

(Submitter supplied) Previous studies indicated that macrophages play a role during lens regeneration in newts, but their function has not been tested experimentally. Here we generated a transgenic newt reporter line in which macrophages can be visualized in vivo. Using this new tool, we analyzed the location of macrophages during lens regeneration. We uncovered early gene expression changes using bulk RNAseq in two newt species, Notophthalmus viridescens and Pleurodeles waltl. more...
Organism:
Pleurodeles waltl
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32009
9 Samples
Download data: CSV, FASTA
Series
Accession:
GSE236906
ID:
200236906
5.

Maternal and zygotic factors sequentially shape the tissue regionalization of chromatin landscapes in early vertebrate embryos

(Submitter supplied) ChIP-seq and RNA-seq analyses to understand the establishment of the cis-regulatory mark H3K4me1 during early embryogenesis.
Organism:
Xenopus tropicalis
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL23182 GPL30018
26 Samples
Download data: NARROWPEAK, TXT
Series
Accession:
GSE172395
ID:
200172395
6.

Mucociliary epidermis RNA-seq data from controls during early patterning (st. 14-20)

(Submitter supplied) This study was conducted to investigate the temporal expression of patterning genes in the Xenopus mucociliary epidermis.
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL22393
6 Samples
Download data: TABULAR, TXT
Series
Accession:
GSE262944
ID:
200262944
7.

Effect of erythropoietin on the gene expression of Xenopus tropicalis peripheral blood cells.

(Submitter supplied) The regulatory system of erythropoiesis through erythropoietin (EPO) and its receptor (EPOR) is essential for vertebrates' life. In humans, EPO affects the erythroid progenitors and stimulates proliferation and differentiation. The EPO-EPOR axis is mainly mediated by the JAK2-STAT5 pathway. After terminal maturation, erythrocytes lost EPOR expression; however, erythrocytes of amphibian Xenopus tropicalis maintain EPOR expression even after their terminal maturation. more...
Organism:
Xenopus tropicalis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL30213
15 Samples
Download data: CSV
Series
Accession:
GSE251901
ID:
200251901
8.

From neural border epithelium to neural crest emigration: A comprehensive single cell roadmap of the timing and regulatory logic underlying cranial and vagal neural crest emergence

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Xenopus laevis; Xenopus tropicalis
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL30018 GPL18936 GPL21875
35 Samples
Download data
Series
Accession:
GSE198494
ID:
200198494
9.

From neural border epithelium to neural crest emigration: A comprehensive single cell roadmap of the timing and regulatory logic underlying cranial and vagal neural crest emergence [morpholinoRNAseq]

(Submitter supplied) Neural crest cells exemplify cellular diversification from a multipotent progenitor population. However, the full sequence of molecular choices governing the emergence of neural crest heterogeneity from the ectoderm remains elusive. Gene regulatory networks govern these steps of embryonic development and cell specification towards definitive neural crest. Here, we combine ultra-dense single cell transcriptomes with machine-learning strategies and experimental validation to provide a comprehensive gene regulatory network driving vertebrate neural crest fate diversification, from induction to early migration stages. more...
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18936
10 Samples
Download data: CSV
Series
Accession:
GSE198493
ID:
200198493
10.

From neural border epithelium to neural crest emigration: A comprehensive single cell roadmap of the timing and regulatory logic underlying cranial and vagal neural crest emergence [ChIPseq]

(Submitter supplied) Neural crest cells exemplify cellular diversification from a multipotent progenitor population. However, the full sequence of molecular choices governing the emergence of neural crest heterogeneity from the ectoderm remains elusive. Gene regulatory networks govern these steps of embryonic development and cell specification towards definitive neural crest. Here, we combine ultra-dense single cell transcriptomes with machine-learning strategies and experimental validation to provide a comprehensive gene regulatory network driving vertebrate neural crest fate diversification, from induction to early migration stages. more...
Organism:
Xenopus laevis; Xenopus tropicalis
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL21875 GPL18936
23 Samples
Download data: CSV
Series
Accession:
GSE198492
ID:
200198492
11.

From neural border epithelium to neural crest emigration: A comprehensive single cell roadmap of the timing and regulatory logic underlying cranial and vagal neural crest emergence [scRNAseq]

(Submitter supplied) Neural crest cells exemplify cellular diversification from a multipotent progenitor population. However, the full sequence of molecular choices governing the emergence of neural crest heterogeneity from the ectoderm remains elusive. Gene regulatory networks govern these steps of embryonic development and cell specification towards definitive neural crest. Here, we combine ultra-dense single cell transcriptomes with machine-learning strategies and experimental validation to provide a comprehensive gene regulatory network driving vertebrate neural crest fate diversification, from induction to early migration stages. more...
Organism:
Xenopus tropicalis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL30018
2 Samples
Download data: PKL
Series
Accession:
GSE198491
ID:
200198491
12.

Mass spectrometry imaging and single-cell transcriptome reveal metabolic profiles of the postauricular glands of the Bufo gargarizans, and hypothesize Bufotoxin biosynthesis pathways

(Submitter supplied) bufotoxin, which contain alkaloids, small peptides and bufadienolides (BDS), are neurotoxic and cardiotoxic, they are promising medical drugs, but the unclear specifics of bufotoxin in the postauricular glands (PG) and the biosynthetic routes of BDS are unknown. We used MALDI/MS to visualize 1872 components of PG, and established the expression profiles of 9316 cells by single-cell sequencing, which were classified into nine clusters by marker genes. more...
Organism:
Bufo gargarizans
Type:
Expression profiling by high throughput sequencing
Platform:
GPL34298
1 Sample
Download data: MTX, TSV
Series
Accession:
GSE261560
ID:
200261560
13.

RNAseq analysis of Xenopus laevis wildtype and emi2 mutant multiciliated cells during and post differentiation

(Submitter supplied) Multiciliated cells (MCCs) form when progenitors massively expand centriole number, yielding the hundreds of basal bodies required to extend multiple motile cilia. This organelle biogenesis is promoted transcriptionally by Multicilin acting in a complex with the E2F transcription factors, which activates the expression of genes known to be involved required to form centrioles during the cell cycle, but also requires a cell cycle state required for the centrosome cycle. more...
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18936
12 Samples
Download data: XLSX
Series
Accession:
GSE195635
ID:
200195635
14.

Sf3b4 mutation in Xenopus tropicalis causes RNA splicing defects and gene dysregulation across development and disrupts cranial neural crest cell migration and survival

(Submitter supplied) Nager syndrome is a rare craniofacial and limb disorder characterized by midface retrusion, micrognathia, absent thumbs, and radial hypoplasia. This disorder results from haploinsufficiency of SF3B4 (splicing factor 3b, subunit 4) a component of the pre-mRNA spliceosomal machinery. The spliceosome is a complex of RNA and proteins that function together to remove introns and join exons from transcribed pre-mRNA. more...
Organism:
Xenopus tropicalis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL30018
17 Samples
Download data: TXT
Series
Accession:
GSE249075
ID:
200249075
15.

Control of poly(A)-tail length and translation in vertebrate oocytes and early embryos

(Submitter supplied) During oocyte maturation and early embryonic development, poly(A)-tail lengths strongly influence mRNA translation. However, how tail lengths are controlled at different developmental stages has been unclear. Here, we performed tail-length and translational profiling of mRNA reporter libraries (each with > 10 million 3ʹ-UTR sequence variants) in frog oocytes and embryos, and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5-mer. more...
Organism:
Danio rerio; Mus musculus; Xenopus laevis; synthetic construct
Type:
Other
4 related Platforms
83 Samples
Download data: TXT
Series
Accession:
GSE241107
ID:
200241107
16.

Transcriptomic analyses identify pathways linking developmental atrazine exposure to altered intestine development

(Submitter supplied) Purpose: Identify gene expression changes in whole intestines of Xenopus laevis embryos exposed to atrazine (35 mg/L) compared to DMSO controls Methods: NF 39 embryos were exposed to 35 mg/L ATR or DMSO control for 24 hours. After 24 hours of exposure, intestines from embryos of each treatment group were dissected from anesthetized embryos with sharpened forceps. The anterior portion of the embryo (including the head, heart, and foregut) were removed and discarded, leaving only the mid-and hindgut portion of the intestine. more...
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL28901
8 Samples
Download data: CSV
Series
Accession:
GSE226434
ID:
200226434
17.

Identification of genes regulated by mechanical tension in Xenopus laevis explants by transcriptome comparison

(Submitter supplied) During gastrulation and neurulation, the chordamesoderm and overlying neuroectoderm of vertebrate embryos converge under the control of a specific genetic programme to the dorsal midline, simultaneously extending along it. However, whether mechanical tensions resulting from these morphogenetic movements play a role in long-range feedback signalling that in turn regulates gene expression in the chordamesoderm and neuroectoderm is unclear. more...
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21046
6 Samples
Download data: XLSX
Series
Accession:
GSE246027
ID:
200246027
18.

BRCA1 and ELK-1 regulate Neural Progenitor Cell Fate in the Optic Tectum in response to Visual Experience in Xenopus laevis tadpoles 

(Submitter supplied) To identify regulators of activity-dependent neural progenitor cell fate, we used RNA-Seq to profile the transcriptomes of proliferating neural progenitor cells and newly-differentiated immature neurons. We identified six DE transcription factors which are predicted to regulate the majority of the other DE transcripts. We investigated the effect of BRCA1 and ELK-1 on activity-regulated neurogenesis in the tadpole visual system and found that knockdown of either BRCA1 or ELK-1 altered the fates of neural progenitor cells, and furthermore that the effects of visual experience on neurogenesis depend on BRCA1 expression, while the effects of visual experience on neuronal differentiation depend on ELK-1 expression. more...
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17682
6 Samples
Download data: FA, GFF3, XLSX
Series
Accession:
GSE184315
ID:
200184315
19.

EcoToxChip 2016 LSARP RNASeq database

(Submitter supplied) As part of the EcoToxChip project, 49 distinct exposure studies were conducted on three lab model species (Japanese quail, fathead minnow, African clawed frog) and three ecologically relevant species (double crested cormorant, rainbow trout, northern leopard frog), at multiple life stages (embryo, adult), exposed to eight chemicals of environmental concern (ethinyl estradiol-EE2, hexabromocyclododecane-HBCD, lead-Pb, selenomethionine-SeMe, 17β trenbolone-TB, chlorpyrifos-CPF, fluoxetine-FLX, and benzo [a] pyrene-BaP. more...
Organism:
Oncorhynchus mykiss; Xenopus laevis; Coturnix japonica; Lithobates pipiens; Phalacrocorax auritus; Pimephales promelas
Type:
Expression profiling by high throughput sequencing
9 related Platforms
724 Samples
Download data: TXT
Series
Accession:
GSE239776
ID:
200239776
20.

Embryos Assist Each Other’s Morphogenesis: calcium and ATP signaling mechanisms in collective resistance to teratogens

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18936
24 Samples
Download data
Series
Accession:
GSE245782
ID:
200245782
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