GEO DataSets

(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) RNA sequencing has allowed high-throughput screening of differential gene expression in many tissues and organisms. Xenopus laevis is a classical embryological and cell-free extract model system, but its genomic sequence had been lacking due to difficulties arising from allotetraploidy. There is currently much excitement surrounding the release of the completed X. laevis genome (version 9.1) by the Joint Genome Institute (JGI), which provides a platform for genome-wide studies. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17682

7 Samples

Download data: TXT, XLSX

(Submitter supplied) Animal embryos have the remarkable property of self-organization. Over 125 years ago Hans Driesch separated the two blastomeres of sea urchin embryos and obtained twins, in what was the foundational experiment of experimental embryology. Since then, embryonic twinning has been obtained experimentally in many animals by diverse methods. In a recent study, we developed bisection methods that generate identical twins reliably from Xenopus blastula embryos. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17682

30 Samples

Download data: XLSX

(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) High-throughput sequencing of small RNAs from Xenopus tropicalis (adult liver, adult skin, oocytes stage I, II, III, IV, V, VI). total RNA, ~18-42 nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

Organism:

Xenopus tropicalis

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9320

5 Samples

Download data

(Submitter supplied) We report the application of paired-end RNA sequencing for high throughput profiling of the Xenopus transcriptome in 23 distinct developmental stages. In total, we obtained over 900 million reads and the deep coverage allowed us to examine the transcriptome in detail. First, we found that ~150 genes are transcribed before embryonic genome activation when transcription is generally thought to be repressed. more...

Organism:

Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15472

40 Samples

Download data: TXT

(Submitter supplied) Purpose: We wished to obtain spatial expression profiles of transcription factor gene expression and expression of other genes. Methods: Embryos were dissected and RNA-seq was performed to determine expression levels of genes. Comparisons between explanted regions permits determination of spatial enrichment of gene expression.

Organism:

Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21874 GPL21875

12 Samples

Download data: TXT

(Submitter supplied) Epigenetic mechanisms set apart the active and inactive regions in the genome of multicellular organisms to produce distinct cell fates during embryogenesis. Here, we report on the epigenetic and transcriptome genome-wide maps of gastrula-stage Xenopus tropicalis embryos using massive parallel sequencing of cDNA (RNA-seq) and DNA obtained by chromatin immunoprecipitation (ChIP-seq) of histone H3 K4 and K27 trimethylation and RNA Polymerase II (RNAPII). more...

Organism:

Xenopus tropicalis

Type:

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

Platform:

GPL9405

4 Samples

Download data: BED, TXT

(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

(Submitter supplied) This study was performed to identify miRNAs that are differentially regulated during mouse kidney development. Two stages (E14.5 and P1) were analyzed. Differential expression was verified using qPCR and/or in situ hybridization.

Organism:

Homo sapiens; Mus musculus; Rattus norvegicus

Type:

Non-coding RNA profiling by array

Platform:

GPL6350

3 Samples

Download data: TXT

(Submitter supplied) To compare nuclear and cytoplasmic RNA from a single cell type, free of cross-contamination, we studied the oocyte of the frog Xenopus tropicalis, a giant cell with an equally giant nucleus. We isolated RNA from manually dissected nuclei and cytoplasm of mature oocytes and subjected it to deep sequencing. Cytoplasmic mRNA 10 consisted primarily of spliced exons derived from ~6700 annotated genes. Nearly all of these genes were represented in the nucleus by intronic sequences. more...

Organism:

Xenopus tropicalis

Type:

Expression profiling by array

Platform:

GPL10263

3 Samples

Download data: CEL

(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:

GPL13741 GPL15472

24 Samples

Download data: TXT

(Submitter supplied) We applied Illumina sequencing to identify microRNAs (miRNAs) and piwi-interacting small RNAs (piRNAs) in the pre- and post-gastrula chicken embryos, and simultaneously obtain a comprehensive expression profile of miRNAs at diverse developmental stages.

Organism:

Gallus gallus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL10223

2 Samples

Download data: 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) Exostosin 1 (Ext1) is a glycosyltransferase involved in the biosynthesis of the extracellular matrix Heparan Sulfate Proteoglycan (HSPG). Knockdown of Ext1 caused gastrulation defects and formation of an abnormal body axis. Since ext1 has been implicated as an indirect contributor to multiple signaling pathways in vertebrate development, microarray was used to identify genes expressed in gastrulae that would be affected by a reduction in ext1 expression. more...

Organism:

Xenopus laevis

Type:

Expression profiling by array

Platform:

GPL10756

6 Samples

Download data: CEL

(Submitter supplied) We performed spatially resolved transcriptomics with sub-single-cell resolution in zebrafish embryos at the one-cell stage, which allowed us to identify a class of mRNAs that is specifically localized at an extraembryonic position in the yolk sac, the vegetal pole. The 3’ UTRs of these localized genes are enriched in specific sequence motifs. Comparison to two frog species revealed relatively low conservation of localized genes, but high conservation of sequence motifs. more...

Organism:

Danio rerio; Xenopus laevis; Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing

4 related Platforms

8 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) Purpose: The establishment of cell lineages occurs via a dynamic progression of gene regulatory networks that underlie developmental commitment and differentiation. To investigate how microRNAs (miRs) function in this process, we compared miRs and miR targets at the initiation of the two major ectodermal lineages in Xenopus. Methods: We injected Xenopus laevis embryos with noggin or constitutively active BMP4 receptor (CABR) at two-cell stage and cut animal caps at stg. more...

Organism:

Xenopus laevis

Type:

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

Platform:

GPL17682

23 Samples

Download data: TXT

(Submitter supplied) Small RNAs play important roles in early embryonic development. However, their expression dynamics and modifications are poorly understood because of the scarcity of RNA that is obtainable for sequencing analysis. Using an improved deep sequencing method that requires as little as 10 ng of total RNA or 50 oocytes, we profile small RNAs in mouse oocytes and early embryos. We find that microRNA (miRNA) expression starts soon after fertilization, and the mature miRNAs carried into the zygote by sperm during fertilization are relatively rare compared to the oocyte miRNAs. more...

Organism:

Homo sapiens; Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL13112 GPL11154

26 Samples

Download data: TXT

(Submitter supplied) Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack a comprehensive understanding of transcript kinetics, which limits quantitative biology. This is an acute challenge in embryonic development where rapid changes in gene expression dictate cell fate decisions. By ultra-high frequency sampling of Xenopus embryos and absolute normalization of sequence reads, we present smooth gene expression trajectories in absolute transcript numbers. more...

Organism:

Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15472

193 Samples

Download data: TXT