GEO DataSets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Xenopus tropicalis

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL15472 GPL13741

9 Samples

Download data

(Submitter supplied) We identified Nodal and Foxh1 downstream targets by performing RNA-seq of embryos either treated with small molecule SB431542 or microinjected morpholino anti-sense oligo against Foxh1.

Organism:

Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13741

4 Samples

Download data: TXT

(Submitter supplied) We defined the genome-wide binding regions of Smad2/3 and Foxh1 at mid-gastrula stage Xenopus tropicalis embryos, at which Nodal signaling and Foxh1 are critical in mesendoderm specification program.

Organism:

Xenopus tropicalis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13741 GPL15472

5 Samples

Download data: TXT

(Submitter supplied) In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic transcription and continuing through gastrulation.

Organism:

Xenopus tropicalis

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL15472 GPL13741

24 Samples

Download data: TXT

(Submitter supplied) The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss of synchronous cell divisions. Little is known about what triggers the activation of transcription or how newly expressed genes interact with each other. Here we use high-resolution expression profiling to identify three waves of gene activity: a post-fertilization wave involving polyadenylation of maternal transcripts; a broad wave of zygotic transcription detectable as early as the 7th cleavage and extending beyond the MBT at the 12th cleavage; and a shorter post-MBT wave of transcription that becomes apparent as development proceeds. more...

Organism:

Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18470 GPL13741

52 Samples

Download data: TXT

(Submitter supplied) Only a minuscule fraction of long non-coding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into their functionality, but comparative analyses have been precluded by our ignorance of lncRNAs in non-model organisms. Here, we use RNA sequencing to identify lncRNAs in eleven tetrapod species and we present the first large-scale evolutionary study of lncRNA repertoires and expression patterns. more...

Organism:

Gallus gallus; Ornithorhynchus anatinus; Xenopus tropicalis; Macaca mulatta; Gorilla gorilla; Homo sapiens; Mus musculus; Monodelphis domestica

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

15 related Platforms

55 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) During embryonic development, maintenance of cell identity and lineage commitment requires the Polycomb-group PRC2 complex, which catalyzes histone H3 K27 trimethylation (H3K27me3). However, the developmental origins of this regulation are unknown. Here, we report on H3K27me3 deposition dynamics in Xenopus embryos, on sequence elements that initiate deposition during pluripotency, and the sequence characteristics that segregate Polycomb-regulated domains from the rest of the genome. more...

Organism:

Xenopus tropicalis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13741 GPL15472

16 Samples

Download data: BED, WIG

(Submitter supplied) To analyze the dynamics and diversity of coding and non-coding transcripts during development, both polyadenylated mRNA and ribosomal RNA-depleted total RNA were harvested across six developmental stages and subjected to high throughput sequencing. The maternally loaded transcriptome is highly diverse and consists of both polyadenylated and deadenylated transcripts. Many maternal genes show peak expression in the oocyte and include genes which are known to be the key regulators of events like oocyte maturation and fertilization. more...

Organism:

Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13741

9 Samples

Download data: CSV

(Submitter supplied) Here we report on genome-wide small RNA and transcriptome profiling of blastula, gastrula and neurula-stage Xenopus tropicalis embryos using deep sequencing. By combining bioinformatic analysis of the small RNA-seq dataset with experimental validation, we identify novel microRNAs and Piwi-interacting RNAs. We show that microRNA expression is highly dynamic and spatially localized in early embryos in contrast to Piwi-interacting RNAs, and we validate a novel microRNA prediction pipeline. more...

Organism:

Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13741

8 Samples

Download data: BED

(Submitter supplied) We defined genome-wide regulatory inputs of the T-box transcription factors Brachyury (Xbra), Eomesodermin (Eomes) and VegT that maintain neuro-mesodermal stem cells and determine their bipotential fates in the Xenopus tropicalis frog embryo.

Organism:

Xenopus tropicalis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13741

10 Samples

Download data: BW

(Submitter supplied) Two-thirds of gene promoters in mammals are associated with regions of non-methylated DNA, called CpG islands (CGIs), which counteract the repressive effects of DNA methylation. In lower vertebrates, computational CGI predictions often reside away from gene promoters, suggesting a major divergence in gene promoter architecture across vertebrates. By experimentally identifying non-methylated DNA in the genomes of seven diverse vertebrates, we instead reveal that non-methylated islands (NMIs) of DNA are a central feature of vertebrate gene promoters. more...

Organism:

Xenopus tropicalis; Homo sapiens; Mus musculus; Anolis carolinensis; Danio rerio; Gallus gallus; Ornithorhynchus anatinus

Type:

Methylation profiling by high throughput sequencing

10 related Platforms

24 Samples

Download data: BED

(Submitter supplied) Transposable elements comprise a large proportion of animal genomes. Transcripts of transposable elements are a source for the synthesis of endogenous siRNAs and piRNAs. In order to determine if small RNAs mapped to expressed Tc1-like elements are present during early Xenopus tropicalis development, we used Illumina (Solexa) to sequence small RNAs from gastrula-stage embryos. We obtained about 17 million reads that mapped perfectly to the genome. more...

Organism:

Xenopus tropicalis

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13741

2 Samples

Download data