Trancriptome study of zebrafish mutant fn10a
Ontology highlight
ABSTRACT:
ORGANISM(S): Danio rerio
PROVIDER: GSE78106 | GEO | 2017/02/10
SECONDARY ACCESSION(S): PRJNA312615
REPOSITORIES: GEO
Similar Datasets
Project description:The zebrafish runzel (ruz) carries a mutation in the titin gene resulting in muscle degeneration and embryonic lethality. At the onset of the visible phenotype (3-3.5 days post fertilization), RNA expression of the tail and trunk (primarily skeletal muscle) was compared between ruz mutants and wildtype siblings using the Affymetrix Zebrafish Gene Chip. Mutant RNA was matched with RNA of wildtype siblings from the same clutch. 3 separate clutches were used (n=3). RNA was labeled, sheered, and hybridized as in Shephard et al. (Shepard et al., 2005) and the data analyzed as in Choe et al. and Weber et al. (Choe et al., 2005; Weber et al., 2005). Results suggest a novel mechanism of titin muscular dystrophy pathogenesis including upregulation of heat shock proteins. Experiment Overall Design: At the onset of the visible phenotype (3-3.5 days post fertilization), RNA expression of the tail and trunk (primarily skeletal muscle) was compared between ruz mutants and wildtype siblings using the Affymetrix Zebrafish Gene Chip. RNA of mutants was matched with RNA of wildtype siblings from the same clutch. 3 separate clutches were used (6 arrays total).
2007-10-05 | E-GEOD-4585 | biostudies-arrayexpress
Project description:MyD88 is an adaptor protein in Toll-like receptor and interleukin 1 receptor mediated signaling pathways that plays an essential role in activation of immune responses following pathogen recognition. We investigate that role in the zebrafish embryo model by using a zebrafish mutant line that contains a premature stop condon in the gene encoding MyD88, leading to a truncated protein that lacks domains important for its normal function. We infected these MyD88 mutants and wildtype individuals with Salmonella typhimurium and Edwardsiella tarda to compare the resulting immune response by transcriptome profiling on total RNA isolated from single embryos. The data derived from these microarray experiments confirms the vital role of MyD88 in pathogen recognition and provides many leads for further research. This microarray study was designed to determine the effect of a truncation of the MyD88 protein on the innate immune response of zebrafish embryos during infection with Salmonella typhimurium and Edwardsiella tarda. Embryos used in this study are derived from an incross between parents heterozygous for the mutation. Both homozygous mutants and their wildtype siblings were selected by genotyping after being injected with the bacteria or PBS as control. RNA was isolated from single embryos and each treatment group consisted of three embryos: (1) Homozygous mutants injected with PBS 8 hours post infection (hpi), (2) wildtype siblings injected with PBS 8hpi, (3) S. typhimurium-infected homozygous mutants 8hpi, (4) S. typhimurium-infected wildtype siblings 8hpi, (5) Homozygous mutants injected with PBS 8 hours post infection (hpi) (E.tarda control), (6) wildtype siblings injected with PBS 8hpi (E. tarda control), (7) E. tarda-infected homozygous mutants 8hpi, (8) E. tarda-infected wildtype siblings 8hpi. Embryos were grown at 28.5M-bM-^@M-^S30M-BM-0C in egg water and manually dechorionated at 24 hours post fertilization (hpf). Subsequently, embryos were infected at 28 hpf by micro-injecting 200 colony forming units (CFU) of S. typhimurium SL1027 or E. Tarda FL-F60, or were mock-injected with buffer as a control. After injections embryos were transferred into fresh egg water and incubated for 8 h or 4 days at 28M-BM-0C. After the incubation period, single embryos were snap-frozen in liquid nitrogen and RNA was isolated for microarray analysis. All treatment groups were analyzed using a common reference approach.
2012-12-10 | E-GEOD-39274 | biostudies-arrayexpress
Project description:The zebrafish runzel (ruz) carries a mutation in the titin gene resulting in muscle degeneration and embryonic lethality. At the onset of the visible phenotype (3-3.5 days post fertilization), RNA expression of the tail and trunk (primarily skeletal muscle) was compared between ruz mutants and wildtype siblings using the Affymetrix Zebrafish Gene Chip. Mutant RNA was matched with RNA of wildtype siblings from the same clutch. 3 separate clutches were used (n=3). RNA was labeled, sheered, and hybridized as in Shephard et al. (Shepard et al., 2005) and the data analyzed as in Choe et al. and Weber et al. (Choe et al., 2005; Weber et al., 2005). Results suggest a novel mechanism of titin muscular dystrophy pathogenesis including upregulation of heat shock proteins. Keywords: disease state analysis
2006-07-30 | GSE4585 | GEO
Project description:We conducted a whole genome transcriptome analysis to examine significant gene expression changes in whole zebrafish larvae at 4 dpf between nlrc3l st73 mutants compared with their control siblings.
2022-05-25 | GSE179883 | GEO
Project description:Adults heterozygous for the hi2217 retroviral insertion within the HAI locus (Mathias et al 2007 JCS) were in-crossed for RNA from hi2217 mutants and corresponding WT siblings. Adults heterozygous for the hi1520 retroviral insertion within the Clint1 locus (Dodd et al, 2009) were in-crossed for RNA from hi1520 mutants and corresponding WT siblings. Both hi2217 and hi1520 are mutants with epidermal defects and showing symptoms of chronic inflammation. In this study we aimed to compare the RNA expression changes between Wild-type siblings (a non-inflammatory status) and homozygous mutants (a chronic inflammatory status) for each mutant background (hi2217 and hi1520).
2014-01-31 | GSE28110 | GEO
Project description:To allow identification of differentially expressed genes and transposons in Dnmt3A mutants at 19dpp and 25dpp; mutant and wildtype RNA-Seq experiments were conducted starting from whole testis RNA.
2022-01-25 | GSE162584 | GEO
Project description:MyD88 is an adaptor protein in Toll-like receptor and interleukin 1 receptor mediated signaling pathways that plays an essential role in activation of immune responses following pathogen recognition. We investigate that role in the zebrafish embryo model by using a zebrafish mutant line that contains a premature stop condon in the gene encoding MyD88, leading to a truncated protein that lacks domains important for its normal function. We infected these MyD88 mutants and wildtype individuals with S Mycobacterium marinum to compare the resulting immune response by transcriptome profiling on total RNA isolated from single embryos. Autophagy regulator dram1 was identified as one of the MyD88-dependent genes. This microarray study was designed to determine the effect of a truncation of the MyD88 protein on the innate immune response of zebrafish embryos during infection with Mycobacterium marinum. Embryos used in this study are derived from an incross between parents heterozygous for the mutation. Both homozygous mutants and their wildtype siblings were selected by genotyping after being injected with the bacteria or PBS as control. RNA was isolated from single embryos at 4 days post infection (4 dpi) and each treatment group consisted of three embryos: (1) Homozygous mutants mock-injected with PBS/2%PVP 4 dpi, (2) wildtype siblings mock-injected with PBS/2%PVP 4dpi, (3) M. marinum-infected homozygous mutants 4dpi, (4) M. marinum-infected wildtype siblings 4dpi. Embryos were grown at 28.5M-bM-^@M-^S30M-BM-0C in egg water and manually dechorionated at 24 hours post fertilization (hpf). Subsequently, embryos were infected at 28 hpf by micro-injecting 200 colony forming units (CFU) of Mycobacterium marinum Mma20 bacteria into the caudal vein, or were mock-injected with buffer (PBS/2%PVP) as a control. After injections embryos were transferred into fresh egg water and incubated for 4 days at 28M-BM-0C. After the incubation period, single embryos were snap-frozen in liquid nitrogen and RNA was isolated for microarray analysis. The treatment groups were analyzed using a common reference approach.
2014-06-01 | E-GEOD-49187 | biostudies-arrayexpress
Project description:MyD88 is an adaptor protein in Toll-like receptor and interleukin 1 receptor mediated signaling pathways that plays an essential role in activation of immune responses following pathogen recognition. We investigate that role in the zebrafish embryo model by using a zebrafish mutant line that contains a premature stop condon in the gene encoding MyD88, leading to a truncated protein that lacks domains important for its normal function. We infected these MyD88 mutants and wildtype individuals with Mycobacterium marinum to compare the resulting immune response by transcriptome profiling on total RNA isolated from single embryos. Autophagy regulator dram1 was identified as one of the MyD88-dependent genes. This RNAseq analysis was used to determine the effect of a truncation of the MyD88 protein on the innate immune response of zebrafish embryos during infection with Mycobacterium marinum. Myd88 mutant and wild type embryos were derived by incrossing homozygous myd88 mutant parents (allele hu3568, van der Vaart et al., 2013, Disease models & mechanisms 6, 841-854) or their wildtype siblings. RNA was isolated from pools of 20 embryos at 4 days post infection (4 dpi). The following treatment groups were used: homozygous mutants mock-injected with PBS/2%PVP 4 dpi, (2) wildtype siblings mock-injected with PBS/2%PVP 4dpi, (3) M. marinum-infected homozygous mutants 4dpi, (4) M. marinum-infected wildtype siblings 4dpi. Embryos were grown at 28.5M-bM-^@M-^S30M-BM-0C in egg water and manually dechorionated at 24 hours post fertilization (hpf). Subsequently, embryos were infected at 28 hpf by micro-injecting 200 colony forming units (CFU) of Mycobacterium marinum Mma20 bacteria into the caudal vein, or were mock-injected with buffer (PBS/2%PVP) as a control. After injections embryos were transferred into fresh egg water and incubated for 4 days at 28M-BM-0C. After the incubation period, single embryos were snap-frozen in liquid nitrogen and RNA was isolated for RNAseq analysis.
2014-06-01 | E-GEOD-49186 | biostudies-arrayexpress
Project description:The transcriptome of larval carcasses from both wildtype and Nxt1 trans-heterozygotes were assessed by RNA-Seq. A total of 1821 genes were down-regulated and 1339 genes were up-regulated. Down-regulated genes had a higher total intron length and had more introns, while up-regulated genes had a lower total intron length and less introns when compared to the non-differentially expressed genes. The majority of down-regulated genes were involved in the production of circular RNAs (circRNAS). We further investigated circRNA expression in larval carcasses from both wildtype and Nxt1 trans-heterozygotes by sequencing total RNA after RNAseR treatment. RNAseR digests linear RNA and thus enriches for circRNAs. Mock samples without RNAseR treatment were also sequenced. We found that circRNA products of Nxt1-responsive genes are reduced in Nxt1 mutants, although the nascent transcripts of these genes are produced at normal levels.
2019-08-09 | GSE135591 | GEO
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