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Spatiotemporal transcriptomic profiling (TOMO-seq) of transcriptomic dynamics during early development of rainbow trout and zebrafish

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Danio rerio Oncorhynchus mykiss

PROVIDER: GSE304790 | GEO | 2026/01/08

REPOSITORIES: GEO

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Spatiotemporal transcriptomic profiling (TOMO-seq) of transcriptomic dynamics during early development of rainbow trout and zebrafish

Project description:Spatiotemporal transcriptomic profiling (TOMO-seq) of transcriptomic dynamics during early development of rainbow trout and zebrafish

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Cloning and characterization of microRNAs from rainbow trout (Oncorhynchus mykiss): their expression during early embryonic development.

Project description:BackgroundCurrent literature and our previous results on expression patterns of oocyte-specific genes and transcription factors suggest a global but highly regulated maternal mRNA degradation at the time of embryonic genome activation (EGA). MicroRNAs (miRNAs) are small, non-coding regulatory RNAs (19-23 nucleotides) that regulate gene expression by guiding target mRNA cleavage or translational inhibition. These regulatory RNAs are potentially involved in the degradation of maternally inherited mRNAs during early embryogenesis.ResultsTo identify miRNAs that might be important for early embryogenesis in rainbow trout, we constructed a miRNA library from a pool of unfertilized eggs and early stage embryos. Sequence analysis of random clones from the library identified 14 miRNAs, 4 of which are novel to rainbow trout. Real-time PCR was used to measure the expression of all cloned miRNAs during embryonic development. Four distinct expression patterns were observed and some miRNAs showed up-regulated expression during EGA. Analysis of tissue distribution of these miRNAs showed that some are present ubiquitously, while others are differentially expressed among different tissues. We also analyzed the expression patterns of Dicer, the enzyme required for the processing of miRNAs and Stat3, a transcription factor involved in activating the transcription of miR-21. Dicer is abundantly expressed during EGA and Stat3 is up-regulated before the onset of EGA.ConclusionThis study led to the discovery of 14 rainbow trout miRNAs. Our data support the notion that Dicer processes miRNAs and Stat3 induces expression of miR-21 and possibly other miRNAs during EGA. These miRNAs in turn guide maternal mRNAs for degradation, which is required for normal embryonic development.

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Transcriptional profiling during rainbow trout ovarian development

2013-04-11 | GSE39587 | GEO

Tools to Image Germplasm Dynamics During Early Zebrafish Development.

Project description:During the first day of zebrafish development, ribonucleoprotein (RNP) complexes called germplasm form large aggregates that initially segregate asymmetrically during cleavage stages. After zygotic genome activation, the granules break into smaller fragments that associate with the nuclear membrane as perinuclear (germ) granules toward the end of gastrulation. The mechanisms underlying the highly dynamic behavior of germ granules are not well studied but thought to be facilitated by the cytoskeleton. Here, we present efficient mounting strategies using 3d-printed tools that generate wells on agarose-coated sample holders to allow high-resolution imaging of multiplexed embryos that are less than one day post-fertilization (dpf) on inverted (spinning disk confocal) as well as upright (lattice light-sheet and diSPIM) microscopes. In particular, our tools and methodology allow water dipping lenses to have direct access to mounted embryos, with no obstructions to the light path (e.g., through low melting agarose or methyl cellulose). Moreover, the multiplexed tight arrays of wells generated by our tools facilitate efficient mounting of early embryos (including cleavage stages) for live imaging. These methods and tools, together with new transgenic reporter lines, can facilitate the study of germ granule dynamics throughout their lifetime in detail, at high resolution and throughput, using live imaging technologies.

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Transcriptional profiling during rainbow trout ovarian development

Project description:The study aimed to characterize gene expression in rainbow trout ovary during ovarian development from immature to mature stages. Whole ovary were collected at the following stages: immature pre-vitelogenesis (IMM), mid-vitellogenesis (MV), late vitellogenesis (LV), post-vitellogenesis (PV) and mature while meiotic maturation is in progress (MAT). Gene expression in rainbow trout ovary was measured at 5 different stages (immature, mid-vitellogenesis, late vitellogenesis, post-vitellogenesis and mature). Three to four biological replicates were used for each stages.

2013-04-11 | E-GEOD-39587 | biostudies-arrayexpress

miRNA transcriptional profiling during rainbow trout ovarian development

2013-04-11 | GSE39588 | GEO

miRNA transcriptional profiling during rainbow trout ovarian development

Project description:The study aimed to characterize miRNA expression in rainbow trout ovary during ovarian development from immature to mature stages. Whole ovary were collected at the following stages: immature pre-vitelogenesis (IMM), mid-vitellogenesis (MV), late vitellogenesis (LV), post-vitellogenesis (PV) and mature while meiotic maturation is in progress (MAT). miRNA expression in rainbow trout ovary was measured at 5 different stages (immature, mid-vitellogenesis, late vitellogenesis, post-vitellogenesis and mature). Two to three biological replicates were used for each stages.

2013-04-11 | E-GEOD-39588 | biostudies-arrayexpress

Single-cell transcriptomic analysis of zebrafish cranial neural crest reveals spatiotemporal regulation of lineage decisions during development.

Project description:Neural crest (NC) cells migrate throughout vertebrate embryos to give rise to a huge variety of cell types, but when and where lineages emerge and their regulation remain unclear. We have performed single-cell RNA sequencing (RNA-seq) of cranial NC cells from the first pharyngeal arch in zebrafish over several stages during migration. Computational analysis combining pseudotime and real-time data reveals that these NC cells first adopt a transitional state, becoming specified mid-migration, with the first lineage decisions being skeletal and pigment, followed by neural and glial progenitors. In addition, by computationally integrating these data with RNA-seq data from a transgenic Wnt reporter line, we identify gene cohorts with similar temporal responses to Wnts during migration and show that one, Atp6ap2, is required for melanocyte differentiation. Together, our results show that cranial NC cell lineages arise progressively and uncover a series of spatially restricted cell interactions likely to regulate such cell-fate decisions.

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Transcriptional and miRNA profiling during rainbow trout ovarian development

Project description:This SuperSeries is composed of the SubSeries listed below.

2013-04-11 | GSE39590 | GEO

Transcriptional and miRNA profiling during rainbow trout ovarian development

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-04-11 | E-GEOD-39590 | biostudies-arrayexpress