Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1217389 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32178106_1.fastq.gz | Fastqsanger.gz | |||
| SRR32178106_2.fastq.gz | Fastqsanger.gz |
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Project description:Neurobehavioral phenotypes in the pan-neuronal GAL4 zebrafish line Tg(elavl3:KalTA4)
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Project description:Neurobehavioral phenotypes in the pan-neuronal GAL4 zebrafish line Tg(elavl3:KalTA4)
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Project description:The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish, the Tg(elavl3:KalTA4) (HuC) line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tg(elavl3:KalTA4) zebrafish larvae compared to wildtype siblings, which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tg(elavl3:KalTA4) larvae showed alterations in brain activity, brain morphology, and behavior, including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA-seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis, we used economical low-pass whole genome sequencing to map the Tol2-mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga, a known cell cycle regulator, is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan-neuronal lines include the length of the elavl3 (HuC) promoter (9 kb) and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines, we cloned five neuronal promoters (atp6v0cb, elavl3, rtn1a, sncb, and stmn1b) ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase-based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines.
2025-02-02 | GSE288241 | GEO
Project description:The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish, the Tg(elavl3:KalTA4) (HuC) line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tg(elavl3:KalTA4) zebrafish larvae compared to wildtype siblings, which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tg(elavl3:KalTA4) larvae showed alterations in brain activity, brain morphology, and behavior, including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA-seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis, we used economical low-pass whole genome sequencing to map the Tol2-mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga, a known cell cycle regulator, is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan-neuronal lines include the length of the elavl3 (HuC) promoter (9 kb) and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines, we cloned five neuronal promoters (atp6v0cb, elavl3, rtn1a, sncb, and stmn1b) ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase-based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines.
2025-02-04 | GSE288775 | GEO
Project description:The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish, the Tg(elavl3:KalTA4) (HuC) line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tg(elavl3:KalTA4) zebrafish larvae compared to wildtype siblings, which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tg(elavl3:KalTA4) larvae showed alterations in brain activity, brain morphology, and behavior, including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA-seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis, we used economical low-pass whole genome sequencing to map the Tol2-mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga, a known cell cycle regulator, is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan-neuronal lines include the length of the elavl3 (HuC) promoter (9 kb) and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines, we cloned five neuronal promoters (atp6v0cb, elavl3, rtn1a, sncb, and stmn1b) ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase-based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines.
2025-07-15 | GSE302688 | GEO
Project description:Neurobehavioral phenotypes in the pan-neuronal GAL4 zebrafish line Tg(elavl3:KalTA4) - Addition of a second elavl3:KalTA4 bulk RNA-sequencing dataset.
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Project description:Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf Tg((cldnB:GFP);Tg(cldnB:gal4) x Tg(UAS:nicd)) and sibling Tg((cldnB:GFP);Tg(cldnB:gal4)) embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow, we mapped about 26 million sequence reads per sample to the zebrafish genome (build danRer10) and identified 32,105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails, with a fold change ≥0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell-autonomously induces apical constriction and cell adhesion.
2017-01-05 | GSE86571 | GEO
Project description:We previously reported that Def (Digestive-organ expansion factor) was a pan-endodermal enriched factor that is essential for the growth of digestive organs in zebrafish using a def mutant line hi429 as model (Chen et al., 2005). To further elucidate Def function, we generated a Def over-expressed zebrafish line, namely Tg (fabp10a:def)-I, in which def expression was under the control of a liver-specific promoter fabp10a. We used microarrays to detail the global programme of gene expression in Tg (fabp10a:def)-I transgenic line compared with wild type zebrafish control, and identified distinct classes of differently regulated genes in Tg (fabp10a:def)-I line.
2013-02-28 | GSE41059 | GEO
Project description:We previously reported that Def (Digestive-organ expansion factor) was a pan-endodermal enriched factor that is essential for the growth of digestive organs in zebrafish using a def mutant line hi429 as model (Chen et al., 2005). To further elucidate Def function, we generated a Def over-expressed zebrafish line, namely Tg (fabp10a:def)-I, in which def expression was under the control of a liver-specific promoter fabp10a. We used microarrays to detail the global programme of gene expression in Tg (fabp10a:def)-I transgenic line compared with wild type zebrafish control, and identified distinct classes of differently regulated genes in Tg (fabp10a:def)-I line. Total RNA from the adult livers of three independent batches of 3-month-old Tg(fabp10a:def)-I and wild type (AB strain) male fish was extracted using TRIzol (Invitrogen), each batch with the liver samples from three fish mixed together. The samples were subjected to microarray hybridization and the data were generated for further analysis.
2013-02-28 | E-GEOD-41059 | biostudies-arrayexpress
Project description:Neuronal Elavl-like (nElavl) RNA binding proteins have three paralogs (Elavl2, Elavl3 and Elavl4) in the mouse genome. This family of RNABPs have been implicated in a variety of post-transcriptional RNA processing mechanisms, including regulation of mRNA stability, alternative splicing, and translational regulation. In this study, using mouse exon arrays, we identify significant differences (p<0.01) in 119 transcripts between wild-type and Elavl3/Elavl4 double knockout forebrain tissue at postnatal day 0. A total of 10 samples were analyzed. These samples consisted of 5 littermate pairs of wild-type and Elavl3/Elavl4 double knockout mice.
2013-01-05 | E-GEOD-43287 | biostudies-arrayexpress