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Zebrafish foxc1a is required for appendage specific neural circuit development

ABSTRACT: RNA-seq analysis of zebrafish foxc1a mutant

ORGANISM(S): Danio rerio

PROVIDER: GSE64125 | GEO | 2015/03/05

SECONDARY ACCESSION(S): PRJNA270226

REPOSITORIES: GEO

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Zebrafish foxc1a is required for appendage specific neural circuit development

Project description:RNA-seq analysis of zebrafish foxc1a mutant For RNA-seq, mRNA was extracted from 38-40 hpf old embryos. We isolated wild type and foxc1a mutant samples by dissecting the entire first 6 anterior somitic segments (AS) through which the fin nerves migrate, and the adjacent posterior segments (PS; segments 7 through ~12) devoid of fin innervating nerves. Heads and yolks were excluded from all samples. Tissues were stored in RNAlater solution (Life Technologies) for up to 2 days at 4 degree before RNA was extracted using the RNAeasy kit (Qiagen) according to the manufactureM-bM-^@M-^Ys protocol. RNA was tested for integrity using a Bioanalyzer (Agilent technologies). RNA samples showing RIN value of 8 or higher were used for generating cDNA libraries as described in the TruSeqM-BM-. Stranded mRNA sample preparation guide. At the final stage, 15 cycles of PCR amplifications was performed. Barcoded libraries representing duplicates of AS and PS samples of wild type and mutants were validated using Bionalyzer (Agilent Technology) and finally sequenced in Illumina HiSeq 2500 yielding paired end reads of 100bp. The RNA-seq Unified Mapper (RUM) (Grant et al., 2011) was used to align the reads to the Zv9/danRer7 reference genome and to assign each read uniquely to a transcript. We investigated transcripts that showed the highest fold changes of expression between the different groups. For Gene Ontology annotations, genes tagged by the GO term M-bM-^@M-^\axon guidanceM-bM-^@M-^] were obtained from the gene ontology database (http://www.geneontology.org/). Next we filtered this list for the M-bM-^@M-^\Danio rerioM-bM-^@M-^] taxon (resulting in 116 unique genes) and used them to annotate our RNA-seq results.

2015-03-05 | E-GEOD-64125 | biostudies-arrayexpress

Zebrafish foxc1a drives appendage-specific neural circuit development.

Project description: Not available

| S-EPMC4325381 | biostudies-literature

Cavin4/Murc is required for skeletal muscle development and function in zebrafish

Project description:To understand the underlying cause of the swimming defect in Cavin4/Murcb deficient larvae, we isolated mRNA from mutant and sibling zebrafish at 72 hpf and subjected it to microarray analysis. RNA and gDNA were extracted from individual larvae at 72 hpf using Trizol (Life Technologies). Following genotyping, the aqueous phases from at least 10 Trizol extractions were combined by genotype and purified over microspin columns (ZymoResearch). RNA expression from heterozygous and mutant larvae was analyzed by single-color microarray (8x60K Zebrafish Array XS, Oaklabs, Germany).

2015-07-14 | E-GEOD-70858 | biostudies-arrayexpress

Cavin4/Murc is required for skeletal muscle development and function in zebrafish

2015-07-14 | GSE70858 | GEO

Zebrafish arl6ip1 is required for neural crest development during embryogenesis.

Project description: Not available

| S-EPMC3298456 | biostudies-literature

mbnl mutant zebrafish RNA-Seq experiments

Project description:mbnl mutant zebrafish RNA-Seq experiments

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Potential role of hoxb1b in zebrafish development

Project description:identification of differentially expressed genes in hoxb1b homozygous mutant hindbrain when compared to wildtype in zebrafish

2018-07-15 | GSE113398 | GEO

V-ATPase proton pumping activity is required for adult zebrafish appendage regeneration.

Project description: Not available

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shox2 is required for inner ear development

Project description:Zebrafish tissue around the inner ear was dissected from wild-type, heterozygote and mutant ~16-22 hpf embryos and subjected to single cell RNAseq

2023-02-22 | GSE197270 | GEO

WhiB4 is required for the reactivation of latent infection of Mycobacterium marinum in zebrafish [zebrafish RNAseq]

Project description:Granulomas are the pathological hallmark of tuberculosis (TB). In individuals latently infected with Mycobacterium tuberculosis (M. tb), the bacteria are thought to reside within the granulomas in a nonreplicating dormant state due to the lack of oxygen and nutrients. However, a portion of these individuals will develop active TB and little is known on the bacterial mechanisms/factors involved in this process. In this study, we found that WhiB4, an oxygen sensor and a transcription factor, plays a critical role in disease progression and reactivation of Mycobacterium marinum (M. marinum) infection in zebrafish. We show that the whiB4 mutant of M. marinum caused latent infection in adult zebrafish, which is characterized by the stable bacterial loads, constant number of non-necrotized granulomas in fewer organs, and reduced immune responses compared to zebrafish infected with the wild type bacteria or the complemented strain. The mutant bacteria in zebrafish were also less responsive to antibiotic treatments. Moreover, the whiB4 mutant was defective in resuscitation from hypoxia-induced dormancy and that the DosR regulon was dysregulated in the mutant. Taken together, our results suggest that WhiB4 is a major driver of reactivation from latent infection and that WhiB4 is an attractive target for the development of novel therapeutics, which may help to prevent the reactivation of latent infection thereby reducing the incidences of active TB.

2021-06-16 | GSE178186 | GEO

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