Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

High-throughput sequencing of mRNA from oocyte, 1 cell, 16/32 cells, 128/256 cells, 3.5hpf and 5.3hpf zebrafish embryos (Wild type; AB line)

ABSTRACT: mRNA seq based approach to determine the transcriptome dynamics during early development To study the mechanisms regulating this developmental event in zebrafish, we applied RNA deep sequencing technology and generated comprehensive transcriptome profiles of 6 developmental stages from oocyte to early gastrulation. We determined the expression levels of maternal and zygotic transcripts and clustered them based on expression pattern. We identified a large number of novel transcribed regions in un-annotated regions of the genome, as well as splice variants with an estimated frequency of 40-75% during early zebrafish embryogenesis. Our data constitute a useful resource for developmental studies, gene discovery, and genome annotation.

ORGANISM(S): Danio rerio

PROVIDER: GSE22830 | GEO | 2011/03/31

SECONDARY ACCESSION(S): PRJNA127881

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

High-throughput sequencing of mRNA from oocyte, 1 cell, 16/32 cells, 128/256 cells, 3.5hpf and 5.3hpf zebrafish embryos (Wild type; AB line)

Project description:mRNA seq based approach to determine the transcriptome dynamics during early development To study the mechanisms regulating this developmental event in zebrafish, we applied RNA deep sequencing technology and generated comprehensive transcriptome profiles of 6 developmental stages from oocyte to early gastrulation. We determined the expression levels of maternal and zygotic transcripts and clustered them based on expression pattern. We identified a large number of novel transcribed regions in un-annotated regions of the genome, as well as splice variants with an estimated frequency of 40-75% during early zebrafish embryogenesis. Our data constitute a useful resource for developmental studies, gene discovery, and genome annotation. RNA was extracted from pooled embryos of desired stages and one RNA seq library was generated for each sample. Totally 6 stages were selected: Maternal, 1cell, 16/32 cells, 128/256 cells, 3.5hpf and 5.3hpf

2011-03-31 | E-GEOD-22830 | biostudies-arrayexpress

Transcriptomics of Rat Striata 16 h after Gamma Knife Surgery: Distinct Bilateral Effects in the Un-irradiated Striatum

Project description:Gamma knife surgery (GKS) is used for treatment of various brain disorders. The effects of gamma irradiation to targeted and un-targeted regions were evaluated by monitoring gene expression changes in the unilateral irradiated (60 Gy) and contralateral un-irradiated striata in the rat. Striata of irradiated and control brains were dissected 16 h post-irradiation for analysis by rat whole genome 44K DNA oligo microarray. Results revealed 230 induced and 144 repressed genes in the irradiated striatum and 432 induced and 239 repressed genes in the un-irradiated striatum. The number of altered genes in un-irradiated striatum was more than that in irradiated striatum. Results of RT-PCR and western analyses suggested that gamma-irradiation caused cellular damage, including oxidative stress, in both striata of both hemispheres. Our present results indicate that unilateral irradiation during GKS produce bilateral effects as early as 16 h, the time-period analyzed, and these molecular changes in the un-irradiated striatum are ample proof.

2008-10-18 | GSE13220 | GEO

This study examined gene expression in zebrafish embryos exposed to 0 (0.01% DMSO), 16 µM, or 32 µM perfluorobutane sulfonate.

Project description:The objective of this study is to compare the toxicity of the emerging replacement surfactant PFBS to the legacy chemical PFOS in the developing pancreas. Because of its chemical properties, it is hypothesized that PFBS would result in fewer or more mild aberrant pancreas phenotypes and ameliorated pancreas gene expression compared to PFOS. Herein, we use transgenic zebrafish models to visualize these processes in vivo throughout the developmental process, and use RNA-Seq to examine major pathways affected by these embryonic exposures.

2019-02-13 | GSE114356 | GEO

Danio rerio strain:AB/Wild-type

Project description:Single-nucleus chromatin landscapes during zebrafish early embryogenesis

| PRJNA987386 | ENA

FIGLA, an oocyte-specific transcription factor, affects ovarian gene expression

Project description:Ovarian folliculogenesis in mammals is a complex process involving cross talk between germ and somatic cells. Carefully orchestrated expression of transcription factors, cell adhesion molecules and growth factors are required for success. We have identified a germ-cell specific basic helix-loop-helix transcription factor, FIGLA (Factor In GermLine, Alpha) and demonstrated its involvement in two independent developmental processes: formation of primordial follicle and coordinate expression of zona pellucida genes. Taking advantage of Figla null mouse line, we have used microarrays to identify potential downstream target genes. Using high stringent cut offs, we find that FIGLA functions a key regulatory molecule in coordinating expression of the NALP family of genes, genes of known oocyte-specific expression and a set of functionally un-annotated genes. These data implicate FIGLA as a central regulator of oocyte-specific genes that play role in folliculogenesis and early development. Keywords: Time Course; genetic modification

2007-08-17 | GSE5558 | GEO

AB family 1

Project description:Array comparative genomic hybridization was used to identify genomic differences between male and female zebrafish. No universal sex-linked CNVR was identified. AB strain of zebrafish were used.The family consist of the parents and 2 male and female offspring each (total 6 samples). Dad's gDNA was used as reference sample for each family.

2012-04-16 | E-GEOD-34334 | biostudies-arrayexpress

AB family 2

2012-04-16 | E-GEOD-34335 | biostudies-arrayexpress

AB family 2

Project description:Array comparative genomic hybridization was used to identify genomic differences between male and female zebrafish. No universal sex-linked CNVR was identified.

2012-04-17 | GSE34335 | GEO

AB family 1

Project description:Array comparative genomic hybridization was used to identify genomic differences between male and female zebrafish. No universal sex-linked CNVR was identified.

2012-04-17 | GSE34334 | GEO

16-32-00914

Project description:16-32-00914 Map

| PRJNA446039 | ENA