Danio rerio
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA342172 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR4191730.fastq.gz | Fastqsanger.gz | |||
| SRR4191731.fastq.gz | Fastqsanger.gz | |||
| SRR4191729.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 3 of 3 |
Similar Datasets
Project description:To get insights into domain organization and functioning of the Danio rerio major α/β-globin locus (Mα/βGL), we have characterized profiles of histone H3 panacetylation across this locus in erythrocytes of adult fish and 18 dpf larvas. To identify enriched domains in our ChipSeq data we used our original protocol and peak caller MACS2. Histone acetylation profiles of Mα/βGL for adult and embryo cells reveal a breaking point in upstream region of the first embryo-larval gene βe1.There are two sub-segments of acetylation: sub-segment to the left of βe1 harbors adult-specific globin genes and is acetylated only in adult cells. Embryo sub-segment contains embryo-larval globin genes and is located to the right of βe1 gene. Acetylation in this subsegment was detected only in 18 dpf larva. Acetylation profile in adult subs-egment possess largest acetylation domain which covers two pairs of adult-stage globins: αa1, and βa1. High acetylation level in this domain well correlates with high expression level observed for these 4 genes in adult erythrocyte. Pattern of H3 panacetylation in 18 dpf larval erythrocytes differs strikingly from that for adult cells. Embryo-larval segment is fragmented in small domains co-located with gene bodies with gaps in intergenic regions. Adult subsegment in adult cells contains strong acetylation domain that cover 4 globin genes along with a part of intergenic regions and few smaller domains. Alternative stage-specific acetylation of subdomains and different pattern of embryonic-larval and adult domain acetylation strongly support the hypothesis of deep structural and functional segregation of stage-specific subdomains within Mα/βGL locus in zebrafish.
2017-01-01 | GSE86548 | GEO
Project description:In genomes of modern fish and amphibia α- and β- globin genes are grouped at a single locus that may resemble the ancestral one and is syntenic to α-globin locus of modern warm-blooded vertebrates. In Danio rerio, the major locus of α/β globin genes comprises two subclusters, one of them harboring genes expressed in adult and the other – genes expressed in embryonic and larval erythrocytes. The results of our previous study suggested that the adult subcluster of this locus has evolved into α-globin gene domain of vertebrate animals. Here we studied how adult and embryo-larval genes of Danio rerio major globin gene locus are repressed in fibroblasts. The results obtained suggest that that at least some of the globin genes present within the adult subcluster are repressed by Polycomb similarly to human α-globin genes. Furthermore, within two α/β gene pairs repression of α-type and β-type genes appears to be mediated by different mechanisms as increasing the level of histone acetylation can activate transcription of only β-type genes.
2020-07-17 | GSE154562 | GEO
Project description:We have demonstrated that, in developing Danio rerio, the embryo-larval and adult subloci of the major globin locus acquire stage-specific hyperacetylation of histone H3 and that H3 hyperacetylation profiles differ significantly between the embryo-larval sublocus (high level of acetylation within gene bodies but not in intergenic regions) and adult sublocus (extended domains of H3 acetylation covering both gene bodies and intergenic regions). The spatial organization of the two subloci is also found to be different. Whereas the adult sublocus is organized into a relatively compact contact domain, the embryo-larval sublocus has a rather low density of spatial contacts. Finally, we have demonstrated that the conserved upstream enhancer of the locus establishes spatial contacts with transcribed adult genes, but not with transcribed embryo-larval genes, and that the embryo-larval and adult subloci of the major globin gene locus are separated by an insulator colocalizing with a CTCF-binding site.
2017-07-12 | GSE87604 | GEO
Project description:Bekaert2012 - Reconstruction of D.rerio Metabolic Network
Danio rerio
metabolic model accounting for subcellular compartmentalisation (ZebraGEM)
This SBML representation of the D. rerio
(zebrafish) metabolic network is made available under the Creative Commons Attribution-Share Alike 3.0 Unported Licence (see www.creativecommons.org
).
This model is described in the article:
Reconstruction of Danio rerio Metabolic Model Accounting for Subcellular Compartmentalisation.
Bekaert M.
PLoS One. 2012;7(11):e49903.
Abstract:
Plant and microbial metabolic engineering is commonly used in the production of functional foods and quality trait improvement. Computational model-based approaches have been used in this important endeavour. However, to date, fish metabolic models have only been scarcely and partially developed, in marked contrast to their prominent success in metabolic engineering. In this study we present the reconstruction of fully compartmentalised models of the Danio rerio (zebrafish) on a global scale. This reconstruction involves extraction of known biochemical reactions in D. rerio for both primary and secondary metabolism and the implementation of methods for determining subcellular localisation and assignment of enzymes. The reconstructed model (ZebraGEM) is amenable for constraint-based modelling analysis, and accounts for 4,988 genes coding for 2,406 gene-associated reactions and only 418 non-gene-associated reactions. A set of computational validations (i.e., simulations of known metabolic functionalities and experimental data) strongly testifies to the predictive ability of the model. Overall, the reconstructed model is expected to lay down the foundations for computational-based rational design of fish metabolic engineering in aquaculture.
This model is hosted on BioModels Database
and identified by: MODEL1204120000
.
To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. PMID: 20587024
.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to [CC0 Public Domain Dedication>http://creativecommons.org/publicdomain/zero/1.0/] for more information.
2005-01-01 | MODEL1204120000 | BioModels
Project description:Tissues specific transcriptomes of Danio rerio, Danio albolineatus and Danio aesculapii Brain, Liver and Gonads.
2018-11-22 | E-MTAB-7476 | biostudies-arrayexpress
Project description:Studying the effects of propyzamide on Inflammtory Bowel Disease on Danio rerio model
2022-10-10 | GSE194408 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE37163: Gene expression data from time course of fin regeneration in Danio rerio (part 1) GSE37164: Gene expression data from time course of fin regeneration in Danio rerio (part 2) Refer to individual Series
2012-11-01 | E-GEOD-37165 | biostudies-arrayexpress
Project description:The possible benefits of selenium (Se) supplementation are currently under investigation for prevention of certain cancers and treatment of neurological disorders. Little is known concerning the response of the brain to increased dietary Se under conditions of Se sufficiency, despite the majority of Se supplementation trials occurring in healthy subjects considered Se sufficient. We evaluated the transcriptional response of the zebrafish (Danio rerio) brain to supplementation with nutritionally relevant levels of dietary Se (sodium selenite) during conditions of assumed Se sufficiency. We used a microarray approach to analyze the global gene expression response of the brain to dietary Se supplementation for 14 days. The experiment used Affymetrix microarrays to compare whole brain RNA from 8 adult zebrafish (Danio rerio) fed a diet with control selenium levels (1.4ppmSe) and 8 fed a diet supplemented with sodium selenite (5.6ppmSe) for 14 days, and with an equal sex ratio within each diet.
2013-02-26 | E-GEOD-44623 | biostudies-arrayexpress
Project description:comparison of miRNA expression in zebrafish tissues Keywords = miRNA Keywords = microRNA Keywords = zebrafish Keywords = Danio rerio Keywords = development Keywords: other
2005-07-05 | GSE2628 | GEO
Project description:A sequencing-based profiling method (RiboMeth-seq) for ribose methylations was used to study methylation patterns during Zebrafish (Danio rerio) development
2020-10-01 | GSE151797 | GEO