GEO DataSets

(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) A conserved molecular pathway has emerged controlling endoderm formation in Xenopus zebrafish and mice. Key genes in this pathway include Nodal ligands and transcription factors of the Mix-like paired homeodomain class, Gata4-6 zinc finger factors and Sox17 HMG domain proteins. While a linear epistatic pathway has been proposed, the precise hierarchical relationships between these factors and their downstream targets are largely unresolved. more...

Organism:

Xenopus laevis

Type:

Expression profiling by array

Dataset:

GDS2016

Platform:

GPL1318

31 Samples

Download data: CEL, TXT

Analysis of stage 11 embryos inactivated for Nodal signaling, or depleted of Mixer or Sox17 proteins. Microdissected animal caps and vegetal and equatorial regions of stage 11 embryos also examined. Nodal, Mixer, and Sox17 are key proteins of a pathway controlling endoderm formation.

Organism:

Xenopus laevis

Type:

Expression profiling by array, count, 3 development stage, 8 tissue sets

Platform:

GPL1318

Series:

GSE4448

31 Samples

Download data: CEL

(Submitter supplied) We examined the binding dynamics of the maternal TF Foxh1 over a time course of germ layer development. Foxh1 binding was compared to the onset of zygotic transcription (RNA pol II), binding of the co-repressor Tle, Nodal signaling (Smad2/3) and the zygotic endoderm TF Foxa.

Organism:

Xenopus tropicalis

Type:

Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis

Platform:

GPL21875

11 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) Spemann-Mangold organizer-specific transcription factors (TFs), Otx2, Lim1/Lhx1, and Gsc, are essential for embryonic head specification. However, the molecular mechanisms by which those TFs interact with the genome to direct head formation are largely unknown. Here we employed ChIP-seq and RNA-seq approaches in Xenopus tropicalis gastrulae and found that occupancy of the corepressor, TLE/Groucho, is a better indicator of tissue-specific cis-regulatory modules (CRMs) than the coactivator p300, during early embryonic stages. more...

Organism:

Xenopus tropicalis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24898

11 Samples

Download data: BROADPEAK, BW, NARROWPEAK

(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 report the ChIP-seq analysis of multiple Xenopus transcription factors binding. Also, we report loss-of-function transcriptomic analysis of Tcf7l1 by RNA-seq at different developmental stages. These newly generated datasets are analyzed using self-organizing maps, along with previously published Xenopus genomic data.

Organism:

Xenopus tropicalis

Type:

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

Platforms:

GPL21875 GPL24898

19 Samples

Download data: NARROWPEAK, 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) 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) 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 chromatin accessibility and single cell transcriptome analyses to explore the emergence of heterogeneity and underlying gene-regulatory mechanisms during early gastrulation in Xenopus. TF activity was inferred by integrating chromatin accessibility and single cell transcriptomics. Our results show that combinatorial activity of zygotically expressed transcription factors acts on maternally-regulated accessible chromatin to induce organizer gene expression.

Organism:

Xenopus tropicalis

Type:

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

Platforms:

GPL21875 GPL24884

132 Samples

Download data: BED, TAB, TBI, TSV

(Submitter supplied) Studies on the early embryonic development of Xenopus laevis contributed much to the understanding of vertebrate patterning. Gastrula stages are of particular interest because establishment of the axis and germ layer formation take place during these stages. While many genes belonging to several signaling pathways including FGF, Wnt and TGF-beta, have been implicated in patterning the gastrula embryo, the hierarchical interactions between these factors are incompletely known. more...

Organism:

Xenopus laevis

Type:

Expression profiling by array

Platform:

GPL1318

4 Samples

Download data: CEL, CHP

(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

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

1225 Samples

Download data

(Submitter supplied) Mammalian embryogenesis is characterized by rapid cellular proliferation and diversification. Within a few weeks, a single cell zygote gives rise to millions of cells expressing a panoply of molecular programs, including much of the diversity that will subsequently be present in adult tissues. Although intensively studied, a comprehensive delineation of the major cellular trajectories that comprise mammalian development in vivo remains elusive. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

465 Samples

Download data: CSV, MTX