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Transcriptome analysis of wildtype elmo3+/+ and homozygous elmo3-/- knockout zebrafish larvae at 120 hpf through next generation RNA sequencing [dataset 3]

ABSTRACT: Elmo3 is one member of the Elmo protein family. In our study we addressed the question if the functions of Elmo1, Elmo2 and Elmo3 ware consistent or if they differ. With the CRISPR/Cas9 system we generated single knockout mutants of elmo1, elmo2 and elmo3 in the zebrafish. To assess the impact of the loss of one of the proteins on the transcriptome of a developing organism, we did RNA sequencing and transcriptome analysis with elmo1+/+ and elmo1-/-, elmo2+/+ and elmo2-/- and elmo3+/+ and elmo3-/- zebrafish larvae at 120 hours post fertilization. Here we provide the sequencing data of elmo3+/+ and elmo3-/-.

ORGANISM(S): Danio rerio

PROVIDER: GSE197826 | GEO | 2022/07/25

REPOSITORIES: GEO

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Transcriptome analysis of wildtype elmo1+/+ and homozygous elmo1-/- knockout zebrafish larvae at 120 hpf through next generation RNA sequencing [dataset 1]

Project description:Elmo1 is one member of the Elmo protein family. In our study we addressed the question if the functions of Elmo1, Elmo2 and Elmo3 are consistent or if they differ. With the CRISPR/Cas9 system we generated single knockout mutants of elmo1, elmo2 and elmo3 in the zebrafish. To assess the impact of the loss of one of the proteins on the transcriptome of a developing organism, we did RNA sequencing and transcriptome analysis with elmo1+/+ and elmo1-/-, elmo2+/+ and elmo2-/- and elmo3+/+ and elmo3-/- zebrafish larvae at 120 hours post fertilization. Here we provide the sequencing data of elmo1+/+ and elmo1-/-.

2022-07-25 | GSE197824 | GEO

Transcriptome analysis of wildtype elmo2+/+ and homozygous elmo2-/- knockout zebrafish larvae at 120 hpf through next generation RNA sequencing [dataset 2]

Project description:Elmo2 is one member of the Elmo protein family. In our study we addressed the question if the functions of Elmo1, Elmo2 and Elmo3 are consistent or if they differ. With the CRISPR/Cas9 system we generated single knockout mutants of elmo1, elmo2 and elmo3 in the zebrafish. To assess the impact of the loss of one of the proteins on the transcriptome of a developing organism, we did RNA sequencing and transcriptome analysis with elmo1+/+ and elmo1-/-, elmo2+/+ and elmo2-/- and elmo3+/+ and elmo3-/- zebrafish larvae at 120 hours post fertilization. Here we provide the sequencing data of elmo2+/+ and elmo2-/-.

2022-07-25 | GSE197825 | GEO

Polarized Dock Activity Drives Shh-Mediated Axon Guidance

Project description:In the developing spinal cord, Sonic hedgehog (Shh) attracts commissural axons toward the floor plate. How Shh regulates the cytoskeletal remodeling that underlies growth cone turning is unknown. We found that Shh-mediated growth cone turning requires the activity of Docks, which are unconventional GEFs. Knockdown of Dock3 and 4, or their binding partner ELMO1 and 2, abolished commissural axon attraction by Shh in vitro. Dock3/4 and ELMO1/2 were also required for correct commissural axon guidance in vivo. Polarized Dock activity was sufficient to induce axon turning, indicating that Docks are instructive for axon guidance. Mechanistically, we show that Dock and ELMO interact with Boc, the Shh receptor, and that this interaction is reduced upon Shh stimulation. Furthermore, Shh stimulation translocates ELMO to the growth cone periphery and activates Rac1. This identifies Dock/ELMO as an effector complex of non-canonical Shh signaling and demonstrates the instructive role of GEFs in axon guidance.

2024-05-31 | GSE268644 | GEO

Transcriptome analysis of WT and homozygous elmo knockout zebrafish larvae at 120 hpf through next generation RNA sequencing

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-07-25 | GSE197827 | GEO

Differential gene expression in the liver of zebrafish larvae exposed to 1 mM inorganic arsenic from 4-120 hpf

Project description:The goal of this study is to compare gene expression levels in the livers of larval Tg(fabp10:nls-mcherry) exposed to 1 mM inorganic arsenic from 4-120 hpf to the unexposed siblings. Samples were collected from Tg(fabp10:nls-mcherry) zebrafish larvae that were derived from incrossed parents of the same strain. The background of transgenic lines were typically from mixed outcrosses of the transgenics to AB, TAB5, and TAB14 strains when regenerating the lines as the working stocks aged. All samples were collected at approximately 120 hpf - natural spawning at 8:30-9:00AM EST on day zero, samples were collected at 8-10AM EST on day 5.

2017-11-12 | GSE104953 | GEO

Transcriptomic analysis of the liver from control sibling and mutant uhrf1-hi272 zebrafish larvae at 120 hpf treated with DMSO or Palbociclib (PD)

Project description:This study was carried out to compare the changes in gene expression in livers of 120 hpf control sibling and mutant uhrf1-hi272 zebrafish larvae in response to treatment with DMSO or Palbociclib (PD)

2023-07-28 | GSE234993 | GEO

Transcriptomic profiling of zebrafish livers with nAtf6 overexpression at collected at 78 and 120 hpf

Project description:Activting transcription factor 6 (Atf6) is one of three main mediators of the Unfolded Protein Response and it gets cleaved cleaved in the Golgi and its N-terminal consisting of the bZip domain translocates into the nucleus to generate a transcriptional response (nAtf6). This study carries out RNAseq on an established transgenic overexpression of nAtf6 in zebrafish hepatocytes ( tg(fabp10:nAtf6-cherry; cmlc2:GFP)-C allele). Samples were collected at 78 and 120 hpf to detect gene expression changes at early and late time points after nAtf6 is overexpressed.

2019-05-08 | GSE130800 | GEO

Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for 24 hours (collected at 120 hpf)

Project description:Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from 96-120 hours post fertilization (hpf).

2020-06-23 | GSE151291 | GEO

Genome-wide chromatin accessibility and DNA methylation of wildtype zebrafish livers at 120 hpf

Project description:The goal of this study is genomic chromatin accessibility of 120 hpf zebrafish livers by ATAC-Seq. ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) and the DNA methylation profile using reduced representation bisulfite sequencing (RRBS).

2021-07-07 | GSE173792 | GEO

Gene expression analysis of 120 hpf zebrafish livers following 24 hour iAs exposure

Project description:This study was carried out to compare the changes in the gene expression in the liver of 5 day post fertilization zebrafish larvae in response to 24 hour exposure to 1.0 and 1.5mM iAs and to compare this to changes in gene expression as a result of overexpress as3mt in hepatocytes. CL1 CAAX 1.5 = WT larvae exposed to 1.5 mM iAs; CL2 CAAX 1 = WT larvae exposed to 1.5 mM iAs

2020-08-22 | GSE156420 | GEO

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