Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide map of ETS2 binding in gastrula stage Xenopus.laevis embryos

ABSTRACT: Genome-wide map of ETS2 binding in gastrula stage Xenopus.laevis embryos

PROVIDER: PRJNA445381 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR6884606.fastq.gz	Fastqsanger.gz
	SRR6884607.fastq.gz	Fastqsanger.gz
	SRR6884608.fastq.gz	Fastqsanger.gz
	SRR6884609.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

Genome-wide map of ETS2 binding in gastrula stage Xenopus.laevis embryos

Project description:We examined the location of ETS2 biding in gastrula stage Xenopus embryos to identify direct transcriptional targets of the FGF signaling pathway.

2019-03-22 | GSE112249 | GEO

Whole embryo depletion of Taf15 in gastrula and neurula stage Xenopus tropicalis embryos

Project description:We examined the role of Taf15 in in gastrula and neurula stage Xenopus tropicalis embryos.

2021-07-24 | GSE180671 | GEO

SILAC-based quantitative proteomic analysis of Drosophila gastrula stage embryos mutant for fibroblast growth factor signalin

Project description:Quantitative mass spectrometry-based proteomic analyses in combination with genetics provide powerful tools in developmental cell signaling research. Drosophila melanogaster is one of the most widely used genetic models for studying development and disease. Here we combined quantitative proteomics with genetic selection to determine global changes in the proteome upon depletion of the Heartless (Htl) Fibroblast-Growth Factor (FGF) receptor signaling in Drosophila embryos at the gastrula stage. We present a robust, single generation SILAC (stable isotope labeling with amino acids in cell culture) protocol for labeling proteins in early embryos and for the selection of homozygously mutant embryos at pre-gastrula stages using an independent genetic marker. Our analyses detected quantitative changes in the global proteome of htl mutant embryos during gastrulation. We identified distinct classes of down-regulated and up-regulated proteins and network analyses indicates functionally related groups of proteins in each class. In addition, we identified changes in the abundance of phosphopeptides. These data suggest that FGF signaling in the early embryo affects global changes in the abundance of metabolic, nucleoplasmic, cytoskeletal and transport proteins.

2021-09-09 | PXD016438 | Pride

Analysis of miRNA abundance in early gastrula stage lin28 knockdown Xenopus embryos

Project description:The abundance of miRNAs in control Xenopus tropicalis embryos at early gastrula stage 10.5 was compared to that in sibling embryos in which the RNA binding proteins lin28a1, lin28a2 and lin28b have been knocked down by injection of translation blocking antisense morpholino oligos.

2015-10-30 | E-MTAB-3936 | biostudies-arrayexpress

Analysis of miRNA abundance lin28 knockdown Xenopus embryos at late gastrula stage 13

Project description:The abundance of miRNAs in Xenopus tropicalis embryos injected with a standard control morpholino oligo at early gastrula stage 13 was compared to that in sibling embryos in which the RNA binding proteins lin28a1, lin28a2 and lin28b have been knocked down by injection of translation blocking antisense morpholino oligos. A dual colour array system is used for analysis. n Expression levels are determined relative to a common, pooled mixed developmental stage RNA sample.

2015-10-31 | E-MTAB-3939 | biostudies-arrayexpress

Whole embryo depletion of Taf15 in gastrula and neurula stage Xenopus tropicalis embryos

Project description:Whole embryo depletion of Taf15 in gastrula and neurula stage Xenopus tropicalis embryos

| PRJNA749055 | ENA

Single-base resolution methylome of Xenopus laevis embryos

Project description:Here we describe a base-resolution DNA methylation map of Xenopus laevis gastrula (st.10.5) embryos generated by whole genome bisulfite sequencing

2016-08-26 | GSE76247 | GEO

Deep sequencing of small RNAs in the Xenopus tropicalis gastrula

Project description: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. Small RNAs mapped to selected transposable elements were characterized and the expression of selected small RNAs was experimentally verified during development. This is the first deep sequencing experiment for small RNAs in the Xenopus tropicalis gastrula.

2011-06-18 | GSE30067 | GEO

ATAC-seq identifies accessible chromatin domains in gastrula stage Xenopus laevis

Project description:In the embryo, inductive cues are interpreted by competent tissues in a spatially and temporally restricted manner, and the mechanisms for the loss of responsiveness are not well understood. To test the hypothesis that loss of competence is associated with changes in chromatin accessibility, we adapted the assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) for use in Xenopus laevis to evaluate genome-wide changes in chromatin accessibility in early and late gastrula stages. ATAC-seq was performed on presumptive ectoderm (animal caps) explanted at the blastula stage and cultured until siblings reached early (stage 10) or late (stage 12) gastrula stage. Approximately 70,000 accessible regions were identified at intergenic regions, introns, promoters, and transcription termination sites at both stages. Accessibility decreased from stage 10 to stage 12 at 279 promoters, including developmental regulators such as Foxh1, chordin, and VegT. Accessible chromatin domains overlap extensively with previously reported p300 binding sites, consistent with putative cis-regulatory modules (pCRMs), and these pCRMs are enriched for binding motifs for pluripotency factors, including Sox, Oct/Pou, and KLF binding motifs. Dorsal Wnt target gene promoters are not accessible after the loss of competence, but inhibition of histone deacetylases increases acetylation at these promoters and extends competence for dorsal gene induction by Wnt signaling. In contrast, the promoters for genes involved in mesoderm and neural crest development remain open through gastrulation, and histone deacetylase inhibition does not extend competence for mesoderm or neural crest induction. These data suggest that chromatin state regulates the loss of competence to inductive signals in a context-dependent manner.

2020-02-26 | GSE138905 | GEO

Deep sequencing of small RNAs in the Xenopus tropicalis gastrula

2011-06-18 | E-GEOD-30067 | biostudies-arrayexpress