Zebrafish
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA335774 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The goals of this study are to compare NGS in 3day post fertilized zebrafish embryo after knockout terfa (telomere repeats binding factor 2). In order to investigate the role of terfa in DDR, telomere protection and neuro-development. Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the zebrafish genome (build zv10) and identify 8840 NGS in 'WT vs terfa-/-' group and 4137 NGS in 'WT vs terfa+/-' group. Our results indicate that zebrafish terfa involved in 1. cell cycle dysregulation (e.g. senescence, p53, spliceosome, RNA transport, Ribosome, mRNA surveillance and cell cycles), including an increased expression of two p53-targeted genes, cdkn1a (p21) and gadd45; 2. inflammation (e.g. Salmonella and Herpes simplex infections, TOL-like receptor signaling and Cell Adhesion), including an increased expression of two pro-inflammatory genes, il6 and isg15. 3. neuronal dysfunction (e.g. Phototransduction, Calcium signaling and Neuroactive ligand-receptor interaction), including a signature of glial injury (gfap, ctsl, metrn, gcm2, clu and 5 members of the slc1a family (3, 4, 5, 7, 8)).
2022-03-09 | GSE173639 | GEO
Project description:Morus alba L. Raw protein sequence reads and sequence
2024-02-08 | PXD049451 | iProX
Project description:Total RNA was extracted from wild type and mutant zebrafish embryos. Double stranded cDNA representing the 3' ends of transcripts was made by a variety of methods, including polyT priming and 3' pull down on magentic beads. Some samples included indexing test experiments where a sequence barcode was placed within one of the sequence reads. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_phD 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/
2013-05-13 | E-ERAD-84 | biostudies-arrayexpress
Project description:We applied time-series SE50bp RNA-seq with 35M reads per sample in wild-type, MZsox19b, MZspg, and double MZspgsox19b mutants in zebrafish embryos to understand the role of Pou5f3 and Sox19b during zebrafish zygotic genome activation. In total we sequenced 4 biological replicates (rep1-4) for WT time curve and 2 biological replicates (rep1-2) for each mutant. WT rep5 are technical replicates for WT rep1, while MZsox19b rep3 and MZspg rep3 are techical replicates for MZsox19b rep1 and MZspg rep1, respectively.
2021-03-03 | GSE137424 | GEO
Project description:zebrafish intestinal microbiome Raw sequence reads
| PRJNA823740 | ENA
Project description:Purpose: Identify zebrafish control and csf1r-mutant brain transcriptomes Methods: RNA sequencing was performed on whole brain of control (3x), csf1ra-/- microglia (3x) and csf1ra-/-;b+/- microglia (3x) and csf1ra-/-;b-/- zebrafish. 10-20 million reads per sample were obtained. Reads were mapped to zebrafish genome GRC10. Results: We identified that microglia gene expression was reduced in csf1ra-/-;b+/- and csf1ra-/-;b-/;- mutant transcriptomes.
2018-07-20 | GSE116216 | GEO
Project description:This study profiled the transcriptome of zebrafish embryos harboring mutation in the Sin3A associated Protein 130a (sap130a) gene at 36 hours post fertilization (hpf). The sap130a mutant was generated via Cas9 mediated gene editing. Zebrafish sap130a mutants are viable presumable due to the presence of maternal RNA. Generation of maternal zygotic (MZ) mutants resulted in an incomplete penetrance of heart ventricle defects that were visible as early as 36 hpf. In this experiment the MZsap130a mutant embryos were further sorted for embryos with smaller ventricle (SV) vs normal size ventricle (NV). To extend on this study and to specifically analyze the heart, sap130a mutant and WT hearts at 48 hpf were extracted for RNA-seq analysis.
2023-05-31 | GSE228057 | GEO