Dynamic Transcriptional and Chromatin Accessibility Landscape of Medaka Embryogenesis
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PROVIDER: PRJNA560968 | ENA |
REPOSITORIES: ENA
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Project description:Chromatin accessibility of nine embryonic samples was profiled using transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) to identify potential regulatory elements.
2020-06-16 | GSE136027 | GEO
Project description:Using medaka fish embryo model, toxic effects of silver nanocolloids (SNC, 3.8M-BM-11.0nm diameter) on developmental morphology and gene expression profile were investigated. SNC caused morphological changes in embryos including cardiovascular malformations, ischemia, underdeveloped central nervous system and eyes, and kyphosis at exposures of 0.5mg/L and 1.0mg/L.. To determine in vivo distribution of SNC, medaka embryos were exposed to 0.5mg/L for 6 days and subjected to ICP-OES analyses. Silver was detected in medaka embryos and chorion at levels of 16.6M-BM-19.3pg and 720M-BM-129pg, respectively. TEM analyses showed SNC adhered to the chorion surface and inside the chorion. On investigation of oxidative mechanism, NAC (0.05mM) rescued all embryos by 96-hr post treatment, while 0.5mM GSH did not. NAC blocked lipid peroxidation. Furthermore, medaka oligo DNA microarray and qRT-PCR were used for gene expression profiling in embryos exposed for 48-hr to 0.05mg/L SNC. Six genes relative to embryogenesis and morphogenesis such as ctsL, Tpm1, RBP, mt, atp2a1 and hox6b6 turned out to be affected and their involvement to the above malformations was implied. In conclusion, SNC causes gross malformations in the cardiovascular and central nervous systems in developing medaka embryos through potentially SNC-affected differential expression of a series of genes related to oxidative stress, embryonic cellular proliferation, and morphological development. Three of the stage-21 medaka embryos per sample were exposed in triplicate to 0mg/L (control) and 0.05mg/L SNC for 48 hours. Therefore, for each exposure condition nine of the stage-21 embryos were prepared and used in the SNC exposure test.
2012-06-16 | E-GEOD-33488 | biostudies-arrayexpress
Project description:Dynamic chromatin accessibility landscape changes following interleukin-1 stimulation
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Project description:Dynamic chromatin accessibility landscape changes following interleukin-1 stimulation
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Project description:Using medaka fish embryo model, toxic effects of silver nanocolloids (SNC, 3.8±1.0nm diameter) on developmental morphology and gene expression profile were investigated. SNC caused morphological changes in embryos including cardiovascular malformations, ischemia, underdeveloped central nervous system and eyes, and kyphosis at exposures of 0.5mg/L and 1.0mg/L.. To determine in vivo distribution of SNC, medaka embryos were exposed to 0.5mg/L for 6 days and subjected to ICP-OES analyses. Silver was detected in medaka embryos and chorion at levels of 16.6±9.3pg and 720±29pg, respectively. TEM analyses showed SNC adhered to the chorion surface and inside the chorion. On investigation of oxidative mechanism, NAC (0.05mM) rescued all embryos by 96-hr post treatment, while 0.5mM GSH did not. NAC blocked lipid peroxidation. Furthermore, medaka oligo DNA microarray and qRT-PCR were used for gene expression profiling in embryos exposed for 48-hr to 0.05mg/L SNC. Six genes relative to embryogenesis and morphogenesis such as ctsL, Tpm1, RBP, mt, atp2a1 and hox6b6 turned out to be affected and their involvement to the above malformations was implied. In conclusion, SNC causes gross malformations in the cardiovascular and central nervous systems in developing medaka embryos through potentially SNC-affected differential expression of a series of genes related to oxidative stress, embryonic cellular proliferation, and morphological development.
2012-06-17 | GSE33488 | GEO
Project description:Seasonal transcriptional landscape of medaka brain
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Project description:Zebrafish is a popular model for studies of embryonic development. Recent surveys of zebrafish embryogenesis with single-cell transcriptomics have uncovered hundreds of cell types, but the dynamic accessible regions of the genome that determine regulatory programs responsible for the unique identity and function of each cell type during embryogenesis lack detailed study. Here, we present SPATAC-seq: a split-pool ligation-based high-throughput single-cell assay for transposase-accessible chromatin using sequencing. Using SPATAC-seq, we profiled chromatin accessibility in more than 808,046 individual nuclei across 20 developmental stages spanning the sphere stage to the early larval protruding mouth stages in a single experiment. Using this chromatin accessibility map, we identified 604 cell types and inferred their developmental relationships. We also identified 959,040 candidate cis-regulatory elements (cCREs) and delineate development-specific cCREs, as well as transcription factors defining diverse cell identities. Importantly, transient reporter assays confirmed that a majority of tested cCREs exhibited robust enhanced EGFP expression in restricted cell types or tissues. Finally, we explored gene regulatory programs that drive pigment and notochord cell differentiation. Our work provides a comprehensive and valuable open resource for exploring transcriptional regulators that determine cell fate specification in zebrafish embryogenesis.
2024-04-14 | GSE243256 | GEO
Project description:The Dynamic Proteome in Arabidopsis Thaliana Early Embryogenesis
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Project description:Study of context-specific regulation during different developmental time windows of Drosophila melanogaster embryogenesis. Single cell chromatin accessibility was profiled by sciATAC-seq in F1 hybrid embryos obtained by crossing males from four genetically distinct inbred lines from the DGRP collection (Mackay et al. 2012) to females from a common maternal “virginizer” line. F1 embryos were profiled at three key stages of embryonic development: 2-4 hours, 6-8 hours and 10-12 hours after egg laying.
2021-12-21 | E-MTAB-10240 | biostudies-arrayexpress
Project description:Medaka fish is a long standing genetic model organism from the 1930s. Uniquely amongstvertebrates Medaka fish can be routinely inbred from the wild (laboratory mice are inbred, butthis does not happen as a routine process from wild individuals), leading to a large number offully inbred wild-derived strains. As part of a broader collaboration I am part of a project toinbred over 100 wild derived strains of Medaka and use them in a similar manner toArabidopsis and Drosophila wild derived lines.To help explore the phenotyping possibilities in this context, we have taken alreadyestablished wild Medaka lines and done reciprocal F1 crosses between 3 strains, and have 4tissues, and a number of parental tissues, giving a total of 40 samples. By doing RNA-seq onthese tissues we do a number of things:(a) assess the level of allele specific expression in Medaka(b) test whether there is any imprinting (parent of origin) in fish. This is thought to not be thecase, but in fact has not been well tested (not least because getting truly inbred fish is hard)(c) assess the level of random allelic activation in brain(d) assess the feasibility for RNAseq based phenotyping in Medaka, providing preliminarydata for future proposals.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2015-12-08 | E-ERAD-390 | biostudies-arrayexpress