Unknown,Transcriptomics,Genomics,Proteomics

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Effect of wood block enrichment on gene expression data in rat liver and spleen following treatment with cyclophosphamide for 5 days

ABSTRACT: Wood blocks are a suggested form of rodent enrichment, however, if ingested, wood blocks could potentially confound early toxicology results. We used microarrays to determine if transcriptomically, rats treated with cyclophosphamide and administered wood blocks were different from those treated with cyclophosphamide and not allowed access to wood blocks Rats (n=3/group) were dosed orally with 40 mg/kg/day Cyclophosphamide or vehicle. In each group half of the rats were allowed access to wood blocks and the other half were not allowed access to wood blocks. At necropsy the liver and spleen were removed and flash frozen in liquid nitrogen. The frozen organs were homogenized individually in Qiazol and RNA extraction was performed. Using a 5ug input, samples were processed for microarray following the Affymetrix procotol. Samples were hybed to Rat 230 2.0 microarray chips.

ORGANISM(S): Rattus norvegicus

SUBMITTER: Amy Ditewig

PROVIDER: E-GEOD-48407 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The current study uses a transcriptomic approach to identify genes associated with differences in wood density, that are likely to be of value as candidate genes in Sitka breeding programmes for improved wood density. Following extensive wood density analysis from a Sitka spruce (Picea sitchensis (Bong) Carr.) field grown clonal trial, three detailed microarray studies were conducted to compare the transcriptome of cambial tissue from contrasting clonal lines with high and low wood density. Twenty five genes exhibited differential expression, reaching as high as 50 fold, in at least two of the three microarray experiments and this was verified using real-time PCR. Identified genes functioned in cell wall synthesis, transcriptional regulation and plant pathogen defence, amongst others. These results confirm the importance of previously-identified density-related genes, and highlight a number of novel genes with a putative role in wood quality. A wide range of processes influence wood density, but this study has allowed the identification of potential regulators in these pathways. Future studies may now use this information to understand the control of natural variation in wood density, and manipulate the expression of these genes to improve timber quality. The Sitka spruce (Picea sitchensis (Bong) Carr.) âExperiment 35â clonal trial was grown at Newcastleton, Scotland (OS grid reference: NY506881, latitude: 55.1847, longitude: -2.77892) and set up by Forest Research, an agency of the Forestry Commission, which has been described previously (Mboyi and Lee 1999). A total of 750 trees were established from cuttings taken in 1989 of genotypes belonging to 6 unrelated full-sib families with 8 genotypes per family and 15 replicate ramets per genotype. Cambial cell scrapes were taken in summer 2004 when trees were 15 years old. A 5x2cm section of bark was cut away at a height of 1.3m from the ground for each tree selected for microarray analysis. The exposed xylem was immediately excised using a clean sharp razor blade and snap frozen in liquid Nitrogen. Samples were transported to the laboratory and ground in liquid nitrogen using a chilled mortar and pestle and stored at -80oC prior to RNA extraction. RNA was extracted and microarray hybridisation performed as described within.

Project description:By using high-density oligonucleotide arrays, we profiled gene expression in reward-related brain regions of rats that developed escalated cocaine intake after extended access to cocaine (6 h per day). Rats allowed restricted daily access to cocaine (only 1 h) that displayed a stable level of cocaine intake and cocaine naive rats were used for controls. Four analysis methods were compared: Affymetrix microarray suite 4 and microarray suite 5, which use perfect-match-minus-mismatch models, and dchip and rma, which use perfect-match-only models to generate expression values. Results were validated by RT-PCR in individual animals from an independent replication of the experiment. A small number of genes was associated with escalated cocaine intake (ESC genes). Unexpectedly, of the brain regions examined [prefrontal cortex, nucleus accumbens, septum, lateral hypothalamus (LH), amygdala, and ventral tegmental area], the LH was the most transcriptionally responsive in escalation of cocaine intake. Most of the ESC genes identified are also expressed during synaptogenesis and synaptic plasticity and include genes that code for several presynaptic and postsynaptic proteins involved in neurotransmission. These results suggest that LH intrinsic circuitry undergoes a structural reorganization during escalation of cocaine use. This remodeling of LH circuitry could contribute to the chronic deficit in reward function that has been hypothesized to drive the transition to drug addiction. Results also support the value of using multiple analysis strategies to identify the most robust changes in gene expression and to compensate for the biases that affect each strategy. Experiment Overall Design: The experimental design for this study comprised three groups of rats (n = 8) with different daily access to a continuous schedule of i.v. cocaine self-administration (0.25 mg per injection): 0 h access per day (drug-naive control rats), 1 h access per day (ShA rats), or 6 h access per day (LgA rats). Experiment Overall Design: Gene expression profiling was then performed for each dissected brain region by using Affymetrix rat neurobiology arrays.

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Effect of wood block enrichment on gene expression data in rat liver and spleen following treatment with cyclophosphamide for 5 days

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