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Items: 1 to 20 of 4584

1.

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; synthetic construct; Xenopus laevis; Mus musculus
Type:
Other
4 related Platforms
83 Samples
Download data: TXT
Series
Accession:
GSE241107
ID:
200241107
2.

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
3.

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
4.

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
5.

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:
Phalacrocorax auritus; Pimephales promelas; Lithobates pipiens; Oncorhynchus mykiss; Xenopus laevis; Coturnix japonica
Type:
Expression profiling by high throughput sequencing
9 related Platforms
724 Samples
Download data: TXT
Series
Accession:
GSE239776
ID:
200239776
6.

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
7.

Embryos Assist Each Other’s Morphogenesis: calcium and ATP signaling mechanisms in collective resistance to teratogens (Stage 35)

(Submitter supplied) We investigated whether normal embryonic developmental cues are only at the level of cells within the embryo or whether they exist in interactions between embryos. To explore this, we subjected groups of embryos with disruptors of normal development while varying group size. RNA-seq analysis revealed a small set of transcripts specific for teratogen response in large groups but not small ones.
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18936
12 Samples
Download data: CSV, TSV
Series
Accession:
GSE245781
ID:
200245781
8.

Embryos Assist Each Other’s Morphogenesis: calcium and ATP signaling mechanisms in collective resistance to teratogens (Stage 25)

(Submitter supplied) We investigated whether normal embryonic developmental cues are only at the level of cells within the embryo or whether they exist in interactions between embryos. To explore this, we subjected groups of embryos with disruptors of normal development while varying group size. RNA-seq analysis revealed a small set of transcripts specific for teratogen response in large groups but not small ones.
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18936
12 Samples
Download data: TSV, XLSX
Series
Accession:
GSE245780
ID:
200245780
9.

Characterization of regeneration initiating cells during Xenopus laevis tail regeneration

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing; Other
Platforms:
GPL21248 GPL28901
63 Samples
Download data: CSV, JPG, JSON, MTX, PNG, TSV, XLSX
Series
Accession:
GSE245320
ID:
200245320
10.

Characterization of regeneration initiating cells during Xenopus laevis tail regeneration [bulk RNA-Seq 2]

(Submitter supplied) In this experiment, we revealed the critical steps for regeneration initiation. We discovered Regeneration Initiating Cells (RICs) using single cell and spatial transcriptomics of the regenerating Xenopus laevis tail. RICs are formed transiently from the basal epidermal cells and are critical for the modification of the surrounding extracellular matrix to allow for migration of other cell types that promote regeneration. more...
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21248
32 Samples
Download data: XLSX
Series
Accession:
GSE245318
ID:
200245318
11.

Characterization of regeneration initiating cells during Xenopus laevis tail regeneration [bulk RNA-Seq 1]

(Submitter supplied) In this experiment, we revealed the critical steps for regeneration initiation. We discovered Regeneration Initiating Cells (RICs) using single cell and spatial transcriptomics of the regenerating Xenopus laevis tail. RICs are formed transiently from the basal epidermal cells and are critical for the modification of the surrounding extracellular matrix to allow for migration of other cell types that promote regeneration. more...
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21248
27 Samples
Download data: XLSX
Series
Accession:
GSE245317
ID:
200245317
12.

Characterization of regeneration initiating cells during Xenopus laevis tail regeneration [spatial transcriptomics]

(Submitter supplied) In this experiment, we revealed the critical steps for regeneration initiation. We discovered Regeneration Initiating Cells (RICs) using single cell and spatial transcriptomics of the regenerating Xenopus laevis tail. RICs are formed transiently from the basal epidermal cells and are critical for the modification of the surrounding extracellular matrix to allow for migration of other cell types that promote regeneration. more...
Organism:
Xenopus laevis
Type:
Other
Platform:
GPL28901
3 Samples
Download data: CSV, JPG, JSON, MTX, PNG, TSV, XLSX
Series
Accession:
GSE245313
ID:
200245313
13.

Characterization of regeneration initiating cells during Xenopus laevis tail regeneration [scRNA-Seq]

(Submitter supplied) In this experiment, we revealed the critical steps for regeneration initiation. We discovered Regeneration Initiating Cells (RICs) using single cell and spatial transcriptomics of the regenerating Xenopus laevis tail. RICs are formed transiently from the basal epidermal cells and are critical for the modification of the surrounding extracellular matrix to allow for migration of other cell types that promote regeneration. more...
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL28901
1 Sample
Download data: MTX, TSV, XLSX
Series
Accession:
GSE245312
ID:
200245312
14.

Fam46a is a regulator for gene expression in secretory tissues and plays an important role in development and homeostasis

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens; Xenopus laevis
Type:
Expression profiling by array
Platforms:
GPL16686 GPL10756
22 Samples
Download data: CEL
Series
Accession:
GSE108692
ID:
200108692
15.

Fam46a is a regulator for gene expression in secretory tissues and plays an important role in development and homeostasis [Fam46a-MO1]

(Submitter supplied) In early embryonic development, the organiser functions in multiple developmental processes, including neural induction, dorsoventral patterning of the mesoderm, and formation of the axial mesoderm. Chordin is a central molecule for the activity of the Spemann’s organiser and abundantly secreted from the Spemann’s organiser in Xenopus laevis. However, so far, a whole picture of the gene expression profile regulated by Chordin has not been examined. more...
Organism:
Xenopus laevis
Type:
Expression profiling by array
Platform:
GPL10756
12 Samples
Download data: CEL
Series
Accession:
GSE108686
ID:
200108686
16.

Fam46a is a regulator for gene expression in secretory tissues and plays an important role in development and homeostasis [Chordin]

(Submitter supplied) In early embryonic development, the organiser functions in multiple developmental processes, including neural induction, dorsoventral patterning of the mesoderm, and formation of the axial mesoderm. Chordin is a central molecule for the activity of the Spemann’s organiser and abundantly secreted from the Spemann’s organiser in Xenopus laevis. However, so far, a whole picture of the gene expression profile regulated by Chordin has not been examined. more...
Organism:
Xenopus laevis
Type:
Expression profiling by array
Platform:
GPL10756
4 Samples
Download data: CEL
Series
Accession:
GSE108684
ID:
200108684
17.

Eukaryotic cytoplasm is widely structured via mesoscale condensates

(Submitter supplied) Compartmentalization is an essential feature of eukaryotic life and is achieved both via membrane-bound organelles, such as mitochondria, and membrane-less biomolecular condensates (BMCs), such as the nucleolus. Known BMCs typically exhibit liquid-like properties and are visualized by microscopy, on the scale of ~1 μm<sup>1,2</sup>. They have been studied mostly by microscopy, examining select individual proteins. more...
Organism:
Xenopus laevis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL28901
9 Samples
Download data: TXT
Series
Accession:
GSE232651
ID:
200232651
18.

Cohesin and CTCF do not assemble TADs in Xenopus sperm and male pronuclei

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Xenopus laevis; Homo sapiens; Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing; Other
5 related Platforms
28 Samples
Download data: BED, BEDGRAPH, HIC
Series
Accession:
GSE237051
ID:
200237051
19.

Cohesin and CTCF do not assemble TADs in Xenopus sperm and male pronuclei

(Submitter supplied) Paternal genomes are compacted during spermiogenesis and de-compacted following fertilization. These processes are fundamental for inheritance but incompletely understood. We analyzed these processes in the frog Xenopus laevis, whose sperm can be assembled into functional pronuclei in egg extracts in vitro. In such extracts, cohesin extrudes DNA into loops, but in vivo cohesin only assembles topologically-associating domains (TADs) at the mid-blastula transition (MBT). more...
Organism:
Xenopus laevis; Mus musculus; Homo sapiens
Type:
Other
5 related Platforms
19 Samples
Download data: HIC
Series
Accession:
GSE237050
ID:
200237050
20.

Cohesin and CTCF do not assemble TADs in Xenopus sperm and male pronuclei

(Submitter supplied) Paternal genomes are compacted during spermiogenesis and de-compacted following fertilization. These processes are fundamental for inheritance but incompletely understood. We analyzed these processes in the frog Xenopus laevis, whose sperm can be assembled into functional pronuclei in egg extracts in vitro. In such extracts, cohesin extrudes DNA into loops, but in vivo cohesin only assembles topologically-associating domains (TADs) at the mid-blastula transition (MBT). more...
Organism:
Xenopus laevis; Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL18936 GPL17021
9 Samples
Download data: BED, BEDGRAPH
Series
Accession:
GSE237049
ID:
200237049
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