RNA-Seq analysis of hearts in foxc1anju18 mutants and WT zebrafish embryos
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ABSTRACT:
PROVIDER: PRJNA728642 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The goal of this study is to compare the relative expression genes in hearts of foxc1a-null mutants and WT siblings. 96hpf hearts of foxc1anju18 and WT siblings were dissected for total RNA extraction. RNA profiles were generated using Illumina deep sequencing. Our study represents the reduced expression of several trabeculation related signaling pathways and cell processes.
2021-12-05 | GSE174156 | GEO
Project description:We have analysed and compared mRNA expression between wt embryos and embryos deficient for Arid3b in E9.5 hearts, with the aim of identifying differentially expressed genes that could give us a clue to the functions of Arid3b during development.
2014-10-07 | GSE62069 | GEO
Project description:We have analysed and compared mRNA expression between wt embryos and embryos deficient for Arid3b in E9.5 hearts, with the aim of identifying differentially expressed genes that could give us a clue to the functions of Arid3b during development. Hearts were dissected from E9.5 embryos (including the heart tube and the pharyngeal mesoderm and endoderm located beneath). Four wild-type and four mutant embryos were collected and pooled for each of the microarray triplicates.
2014-10-07 | E-GEOD-62069 | biostudies-arrayexpress
Project description:The study compares gene expression profile at several stages post amputation of the adult zebrafish ventricular heart between zebrafish mutants and WT siblings. The first experiment was to identify genes that are activated in response to cardiac injury at 3 and 7 days post amputation (dpa). Dusp6 mutant hearts were reported to show an enhanced regenerative response. For this experiment, bulk RNA seq was obtained from WT and Dusp6 mutant hearts and genes increased at 3 and 7 dpa were identified. The forkhead transcription factor, foxm1, showed increased expression in cardiomyocytes and follow up studies show that it is required to regulate cardiomyocyte proliferation. This was further explored with RNA-seq experiments comparing WT and foxm1 mutant hearts at 3dpa. We identified genes normally expressed in proliferating cells to be decreased in the foxm1 mutants.
2022-06-22 | GSE201139 | GEO
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:Purpose: The goals of this experiments are to analyze the transcriptomic change in dyrk1aakrb1 mutants compared with WT embryos by mRNA-seq technique. Methods: Whole mRNA profiles of 48 hpf WT(+/+) and dyrk1aakrb1 mutants zebrafish embryos were generated by mRNA-seq techinque, in duplicate, using HiSeq 2500 (Illumina, Inc., USA). Results: This analysis identified 222 transcripts as differentially regulated genes (DEG), of which 101 were up-regulated and 121 were down-regulated in dyrk1aakrb1 mutant (more than 2 fold and less than 0.5 fold respectively,; p value< 0.05).
2019-05-20 | GSE111280 | GEO
Project description:Transcriptional profiling of 2.25 dpf (days post fertilzation) zebrafish embryos comparing wildtype (control) to med14 (mediator complex subunit 14) mutants. Goal was to determine the extent to which transcription was affected in med14 mutants by analyzing global gene expression. Background: Mediator is an evolutionarily conserved multi-subunit complex that physically links the RNA polymerase II transcriptional machinery to enhancer bound regulatory factors. While classically described as a core component of the transcriptional machinery, recent evidence suggests that Mediator may have context-dependent roles. In particular, a requirement for Mediator in the maintenance of embryonic and induced pluripotent stem cells has been noted. However, the in vivo consequences of loss of function of many Mediator subunits are unknown. Results: We identified med14, which encodes a Mediator subunit, as the gene affected in the zebrafish logelei (log) mutant. log mutants displayed a morphological arrest by 2 days of embryonic development. Surprisingly, microarray analysis showed that transcription was not broadly affected in log mutants. Transplanted log cells placed into a wild-type environment were able to survive into adulthood, suggesting a lack of global transcriptional defects in Med14-deficient cells. RNAi knockdown of the single med14 ortholog in planarians demonstrated that med14 was required for adult stem cell maintenance and regeneration. A broader assay of Mediator subunits revealed that many were required for stem cell maintenance in planarians. Multiple stem/progenitor cell populations were observed to be reduced or absent in zebrafish med14 mutant embryos, with embryonic fin regeneration defects also evident. Conclusions: Taken together, our results show a critical, evolutionarily conserved, function for Med14 (and perhaps Mediator in general) in evolutionarily conserved in vivo stem cell maintenance and regeneration, distinct from a ubiquitous role in transcription.
2017-02-09 | GSE58042 | 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
Project description:RNA-seq of zebrafish sa12692 mutants against WT controls
| PRJEB32363 | ENA
Project description:Purpose: The goals of this experiments are to analyze the transcriptomic change in dyrk1aakrb1 mutants compared with WT embryos by mRNA-seq technique. Methods: Whole mRNA profiles of 32 hpf WT(+/+) and dyrk1aakrb1 mutants zebrafish embryos were generated by mRNA-seq techinque, in duplicate, using HiSeq 2500 (Illumina, Inc., USA). Results: This analysis identified 354 transcripts as differentially regulated genes (DEG), of which 125 were up-regulated and 229 were down-regulated in dyrk1aakrb1 mutant (more than 2 fold and less than 0.5 fold respectively,; p value< 0.05).
2019-05-20 | GSE123026 | GEO