Project description:Gene expression profile comparing 17-month old wild-type with psen1hu2547 zebrafish. Total RNA from 3-4 brains of 17-month old adult psen1hu2547 or WT fish was extracted using RNeasy mini columns (Qiagen) and quality-checked using NanoDrop 1000 (Thermo Scientific) and formaldehyde gel electrophoresis. cDNA was generated and labeled with Cy3 or Cy5-CTP using the low RNA input linear amplification kit (Perkin-Elmer). Upon purification and fragmentation, labeled cRNA was hybridized to the zebrafish 22K 60-mer oligonucleotide microarray (G2518A-001, Agilent Technologies, Santa Clara, CA, USA) at 65ºC for 17 hours. Three independent biological repeats were performed.
Project description:We generate whole-transcriptome RNA-seq profiles of microglia subpopulations in the adult zebrafish brain (4-month-old) to study their heterogeneity. Cells were isolated as ccl34b.1+mpeg1+ populations or ccl34b.1-mpeg1+ populations from the whole brain of double transgenic TgBAC(ccl34b.1:eGFP);Tg(mpeg1:DsRedx) fish. ccl34b.1+mpeg1+ and ccl34b.1-mpeg1+ microglia were grouped into two distinct clusters in the Principal component analysis (PCA), and we identified substantial differentially-expressed genes between these two microglial populations using the DESeq2 package. To further unveil their differential roles during inflammation, we injected E. coli into the brain ventricles of adult zebrafish and isolated both populations for whole-transcriptome RNA-seq. This RNA-seq profile provides valuable information for dissecting their respective functions in vivo.
Project description:Zebeafish yquem harbors a mutation in the gene encoding uroporphyrinogen decarboxylase (UROD), the fifth enzyme in heme biosynthesis, and was established as a vertebrate model for human hepatoerythropoietic porphyria (HEP). In an effort to investigate the unknown aspects of UROD deficiency pathogenesis, we used a 14,000-oligonucleotide-gene microarray to determine differentially expressed genes in yquem/urod (-/-) and wild type control zebrafish larvae. Keywords: zebrafish, Danio rerio, wild-type yquem, urod, porphyria
Project description:Bulk RNA-seq transcriptional profiling was performed on 6 month post-fertilization bbs2 -/- mutant zebrafish retinas and bbs2 +/+ wild-type siblings to investigate the transcriptional changes that occur during progressive photoreceptor degeneration.
Project description:To understand the role of Pou5f3, Sox19b and Nanog during zebrafish zygotic genome activation, RNA-seq time-series for single, double and triple maternal-zygotic (MZ) zebrafish mutants for Pou5f3, Nanog, Sox19b, as well as the wild-type.
Project description:Heterozygous adults of the zebrafish transgenic line Tg(flk1:RFP)is18 develop tumors in the retina, optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 month old sibling wild type and Tg(flk1:RFP)is18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT (wild type); 3 grossly normal retina from Tg(flk1:RFP)is18/+ were pooled to create Sample PT (pre tumor) and 2 large tumors from Tg(flk1:RFP)is18/+ were pooled to create Sample T (tumor). Each sample was run in an individual lane on the HiSeq system.
Project description:To identify the genes differentially expressed in the zebrafish mibta52b mutant, genome-wide transcriptome analysis was performed using Serial Analysis of Gene Expression (SAGE). 335 transcripts were identified whose expressions were significantly altered in the mibta52b mutant as compared with the wild-type.
Project description:Proteins expressed and exported out of the mycobacterial biofilm cells into granulomatous environment during infection were identified by LC-MS/MS. To this end, adult 5- to 10-month-old female AB wild-type zebrafish (Danio rerio) were infected with 4-day old M. marinum ATCC927 (carrying the pTEC27 plasmid expressing the tdTomato fluorescent protein) cells. After 8 weeks post infection, ten zebrafish were euthanized, and red fluorescent mycobacterial granulomas were carefully dissected from the zebrafish ovaries. Ten granulomas were collected per tube, frozen on dry ice and stored at -80 °C until preparation for proteomics. Altogether, ten replicate samples, each with ten mycobacterial granulomas, were subjected to protein extraction and LC-MS/MS identification.
Project description:We applied RNA-seq to 3-month-old rice (Oryza sativa) shoot apical meristem to investigate the effect of RGA1(d1-1) mutation on the meristem initiation using transcriptome of d1 as compared to wild type plant.