GEO DataSets

Analysis of maternal-zygotic (MZ) dicer mutant embryos that lack miR-430 and mutants rescued with miR-430. MZdicer mutants cannot generate mature miRNAs; miR-430 accumulates during maternal-to-zygotic transition and regulates morphogenesis during early development. Results identify miR-430 targets.

Organism:

Danio rerio

Type:

Expression profiling by array, count, 3 development stage, 2 genotype/variation, 2 protocol sets

Platform:

GPL1319

Series:

GSE4201

15 Samples

Download data: CEL, EXP

(Submitter supplied) MicroRNAs comprise 1-3% of all vertebrate genes, but their in vivo functions and mechanisms of action remain largely unknown. Zebrafish miR-430 is expressed at the onset of zygotic transcription and regulates morphogenesis during early development. Using a microarray approach and in vivo target validation, we find that miR-430 directly regulates several hundred target mRNAs. Targets are highly enriched for maternal mRNAs that accumulate in the absence of miR-430. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Dataset:

GDS1771

Platform:

GPL1319

15 Samples

Download data: CEL, EXP

(Submitter supplied) MicroRNAs regulate gene expression through deadenylation, repression and mRNA decay. However, the contribution of each mechanism in non-steady-state situations remains unclear. We monitored the impact of miR-430 on ribosome occupancy of endogenous mRNAs in wild type and dicer mutants lacking mature miR-430. Our results indicate that miR-430 reduces the number of ribosomes on target mRNAs before causing mRNA decay. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9319

22 Samples

Download data: BED

(Submitter supplied) microRNAs play crucial roles in the early development of an organism. However the regulation of transcription through the action of microRNAs during the initial embyonic development has not been studied. We used microarrays to detail the effect of maternal microRNA mir-34 in regulation of zygotic trancription during the initial stages of Zebrafish embryonic development from one cell stage through the maternal-zygotic transition up to 24 hours post fertilization.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL1319

18 Samples

Download data: CEL

(Submitter supplied) Heterochromatin has important functions in the organization of nuclear structure, the maintenance of genome integrity, and the regulation of gene expression programs1-3. Here, we demonstrate that the genome of the early zebrafish embryo is packaged in an atypical chromatin state that lacks features characteristic of heterochromatin. The heterochromatic histone modification, histone H3 lysine 9 trimethyl (H3K9me3), is undetectable in embryonic chromatin and embryonic nuclei are devoid of condensed chromatin prior to activation of the zygotic genome. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20828

20 Samples

Download data: TDF

(Submitter supplied) We report the m6A methylation maps of zebrafish embryos during early development, and transcriptome-wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A-dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish   MZT, highlighting the critical role of the m6A mRNA methylation in animal development.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL18413

76 Samples

Download data: BED, XLSX

(Submitter supplied) The stability of mRNAs is regulated by signals within their sequences, but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here, we introduce UTR-Seq, a combination of massively parallel reporter assays and regression models, to survey the dynamics of tens-of-thousands of 3’UTR sequences during early zebrafish embryogenesis. UTR-Seq revealed two temporal degradation programs: a maternally encoded early-onset program and a late-onset program that accelerated degradation after zygotic genome activation. more...

Organism:

Danio rerio

Type:

Other

Platforms:

GPL21930 GPL18413

71 Samples

Download data: TXT

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

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL30614 GPL20828

49 Samples

Download data: CSV

(Submitter supplied) Background: Early embryonic developmental programs are guided by the coordinated interplay between maternally inherited and zygotically manufactured RNAs and proteins. Although these processes happen concomitantly and affecting gene function during this period is bound to affect both pools of mRNAs, it has been challenging to study their expression dynamics separately. Results: By employing Slam-seq, a nascent mRNA labeling transcriptomic approach, in a developmental time series we observe that over half of the early zebrafish embryo transcriptome consists of maternal-zygotic genes, emphasizing their pivotal role in early embryogenesis. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL20828

15 Samples

Download data: CSV

(Submitter supplied) To study the function of zebrafish Ybx1 during early embryogenesis, we generated maternal ybx1 (Mybx1) mutant using CRISPR/Cas9 and report the transcriptome-wide changes in comparison to wild-type (WT) embryos. Our analysis reveals a dramatic loss of maternal mRNA decay and zygotic genome activation in Mybx1 embryos during maternal-to-zygotic transition.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

4 Samples

Download data: TXT

(Submitter supplied) We adapted the iCLIP method to zebrafish embryos to investigate activities of Hnrnpa1 during the maternal-to-zygotic transition

Organism:

Danio rerio

Type:

Other

Platform:

GPL14875

13 Samples

Download data: BED

(Submitter supplied) Early embryonic development depends on proper utilization and clearance of maternal transcriptomes. How these processes are spatiotemporally regulated remains unclear. Here we show that nuclear RNA-binding protein Rbm14 and maternal mRNAs co-phase separate into cytoplasmic condensates to facilitate vertebrate blastula-to-gastrula development. In zebrafish, Rbm14 condensates were highly abundant in blastomeres and markedly reduced after prominent activation of zygotic transcription. more...

Organism:

Danio rerio; Mus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL29655 GPL21741

21 Samples

Download data: CSV

(Submitter supplied) MicroRNAs (miRNAs) are noncoding RNAs of approximately 22 nucleotides in length that usually suppress the translation of target messenger RNAs (mRNAs) through partial complementarity to the 3¡¦ untranslated region (3¡¦ UTR) of protein-coding mRNAs in animals. However, there is increasing evidence that miRNAs can also reduce the steady-state levels of their target mRNAs in animals. In this investigation, both miRNA and mRNA profiles from the undifferentiated human embryonic stem cell line hES-T3 (T3ES), hES-T3 derived embryoid bodies (T3EB) and hES-T3 differentiated fibroblast-like cells (T3DF) were quantitatively determined. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

8 Samples

Download data: CEL

(Submitter supplied) Next generation sequencing analysis of small RNA-seq and RNA-seq of successive time intervals during P. hawaiensis embryogenesis

Organism:

Parhyale hawaiensis

Type:

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

Platform:

GPL30308

42 Samples

Download data: SF

(Submitter supplied) We followed the polysomal association of maternal and early zygotic transcriptome over the first few hours of embryonic development, prior to and after MBT. We isolated polysome-associated (bound) and non-polysome-associated (unbound) mRNAs using sucrose gradient centrifugation followed by size fractionation. Using next generation sequencing (RNA-seq), we profiled the transcriptome in polysome-bound and unbound fractions. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

18 Samples

Download data: TXT

(Submitter supplied) The control of mRNA stability plays a central role in regulating gene expression. In metazoans, the earliest stages of development are driven by maternally supplied mRNAs. The degradation of these maternal mRNAs is critical for promoting the maternal-to-zygotic transition of developmental programs, although the underlying mechanisms are poorly understood in vertebrates. Here, we characterized maternal mRNA degradation pathways in zebrafish using a transcriptome analysis and systematic reporter assays. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

6 Samples

Download data: TXT

(Submitter supplied) This series consists of samples taken from HeLa cells transfected with one of 7 (wild-type or mutant) miRNA duplexes and harvested either 12 or 24 hours later. Submitted for Nature publication Lim et al. Keywords = microRNA Keywords: other

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS1858

Platform:

GPL1749

14 Samples

Download data

Analysis of HeLa cells at 12 or 24 hours after transfection with wild type or mutant miR-1 or miR-124. miR-1 is preferentially expressed in heart and skeletal muscle, while miR-124 is preferentially expressed in brain. Results suggest that metazoan miRNAs can reduce the levels of target transcripts.

Organism:

Homo sapiens

Type:

Expression profiling by array, log10 ratio, 7 agent, 2 time sets

Platform:

GPL1749

Series:

GSE2075

14 Samples

Download data

(Submitter supplied) The earliest stage of animal development is controlled by maternally deposited mRNA transcripts and proteins. Once the zygote is able to transcribe its own genome, maternal transcripts are degraded, in a tightly regulated process known as the maternal to zygotic transition (MZT). While this process has been well-studied within model species, we have little knowledge of how the pools of maternal and zygotic transcripts evolve. more...

Organism:

Drosophila melanogaster; Drosophila yakuba; Drosophila ananassae; Drosophila erecta; Drosophila miranda; Drosophila sechellia; Drosophila simulans; Drosophila virilis; Drosophila mauritiana; Drosophila mojavensis; Drosophila pseudoobscura; Drosophila willistoni; Drosophila persimilis; Drosophila santomea

Type:

Expression profiling by high throughput sequencing; Third-party reanalysis

14 related Platforms

119 Samples

Download data: TXT

(Submitter supplied) During early neurogenesis, multiple whole animal gene expression profiling studies revealed widespread changes in developmental mRNA and miRNA abundance in ethanol-exposed embryos. Consistent with a role for miRNAs in neurobehavioral development, miRNA target prediction analyses identified multiple miRNAs misexpressed in the ethanol exposed cohorts that were also predicted to target inversely expressed transcripts known to influence brain morphogenesis.

Organism:

Danio rerio

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platforms:

GPL13832 GPL13318

24 Samples

Download data: PAIR, TXT