Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Xenopus tropicalis

ABSTRACT: High-resolution analysis of gene activity during the Xenopus mid-blastula transition

PROVIDER: PRJNA242712 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR1205740_1.fastq.gz	Fastqsanger.gz
	SRR1205740_2.fastq.gz	Fastqsanger.gz
	SRR1205750_1.fastq.gz	Fastqsanger.gz
	SRR1205750_2.fastq.gz	Fastqsanger.gz
	SRR1205760_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 104

Similar Datasets

High-resolution analysis of gene activity during the Xenopus mid-blastula transition

Project description: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. Our studies have also allowed us to define a set of maternal genes whose mRNAs are deadenylated shortly after fertilization, and are likely to be degraded thereafter. Experimental analysis indicates that the polyadenylation of maternal transcripts is necessary for the establishment of proper levels of zygotic transcription at the MBT, and that genes activated in the second wave of expression, including Brachyury and Mixer, contribute to the regulation of genes expressed in the third. Together, our high-resolution time series and experimental studies have yielded a deeper understanding of the temporal organization of gene regulatory networks in the early Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization

2014-03-27 | E-GEOD-56242 | biostudies-arrayexpress

Pol III chromatin immunoprecipitation-sequencing (ChIP-seq) of Xenopus tropicalis blastula embryos

Project description:To correlate 5fC clusters with RNA polymerase III occupancy genome-wide, we carried out Pol III ChIP-seq profiling in Xenopus tropicalis blastula embryos.

2024-08-29 | GSE226463 | GEO

RNA-seq expression profiling of Xenopus tropicalis blastula embryos upon Tet2 and Tet3 knockdown

Project description:To analyze the role of Tet proteins on global gene expression, we profiled the transcriptome of Xenopus tropicalis blastula embryos upon knockdown of Tet2 and Tet3 using Morpholino antisense oligonucleotides.

2024-08-29 | GSE226466 | GEO

Xenopus tropicalis x Xenopus laevis

Project description:Single-base resolution methylomes of Xenopus laevis x Xenopus tropicalis embryos

| PRJNA356296 | ENA

Nascent transcriptome of Xenopus laevis embryos at mid-blastula transition (MBT) stages

Project description:Nascent transcriptome of Xenopus laevis embryos at mid-blastula transition (MBT) stages

| PRJNA545469 | ENA

High-resolution analysis of gene activity during the Xenopus mid-blastula transition

2014-03-27 | GSE56242 | GEO

A Genome-Wide Survey of Maternal and Embryonic Transcripts during Xenopus tropicalis Development

Project description: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. Of all the transcripts that increase in abundance between an early blastula and larval stages, about 30% of the embryonic genes are induced by fourfold or more by the late blastula stage and another 35% by late gastrulation. Using a gene model validation and discovery pipeline, we identified novel transcripts, the majority of which show hallmarks of being long non-coding RNAs both in terms of their coding potential and gene structure. Profiles of polyadenylated mRNA (6 stages) and ribosomal RNA-depleted total RNA (3 stages) through early Xenopus tropicalis development

2013-11-12 | E-GEOD-43652 | biostudies-arrayexpress

Xenopus tropicalis

Project description:High-throughput sequencing of small RNAs from Xenopus tropicalis

| PRJNA111817 | ENA

DNA immunoprecipitation sequencing (DIP-seq) of Xenopus tropicalis blastula embryos using 5mC, 5hmC, 5fC and 5caC antibodies

Project description:The oxC-marks 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) are iterative oxidation products of 5-methylcytosine (5mC) which might also function as epigenetic marks on their own to regulate gene expression. To characterize the genomic profiles of oxC-marks in Xenopus tropicalis blastula embryos, we carried out DIP-seq using 5mC, 5hmC, 5fC and 5caC antibodies.

2024-08-29 | GSE226465 | GEO

Xenopus tropicalis

Project description:Global gene expression during early differentiation of Xenopus (Silurana) tropicalis gonad tissues.

| PRJNA253012 | ENA