Re the deceased animal was relatively fresh, necropsies were performed to

Re the deceased animal was relatively fresh, necropsies were performed to

Re the deceased animal was relatively fresh, necropsies were performed to determine if tumor was present at time of death. In cases where a tumor could not be confirmed at the time of necropsy, animals were censored for the purposes of survival analysis.Mtap QuantificationMtap protein levels were detected by Western blot analysis using a MTAP monoclonal antibody (Santa Cruz Biotechnology) at a 1/1000 dilution. Signal was visualized by SuperSignal West Pico Chemiluminescent kit (Pierce), and signal was quantified using Alpha Innotech image analyzer. All levels were normalized to an alpha-actin internal control. Mtap expression ,20 that of control samples was scored as Mtap2.Microarray ExperimentsLivers from 100-day-old male Mtap+/+ and MtaplacZ/+ mice were excised and put into RNAlater (Ambion). Total RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA) and further purified by RNeasy kit (Qiagen, Valencia, CA) according to manufacturer’s instructions. RNA quality was evaluated by electrophoresis on Agilent Bioanalyzer (Agilent). Five mg of total RNA was first transcribed into cDNA using the Invitrogen’s Superscript system with an oligo (dT)24 primer containing a T7 RNA polymerase promoter sequence at its 59 end. After double stranded cDNA synthesis using DNA polymerase I, Biotin-labeled cRNA was generated by in 16985061 vitro transcription using a GeneChip IVT Labeling Kit (Affymetrix) according to manufacturer’s instructions and then purified using the GeneChip Cleanup Module. Label target was fragmented to a size of 35?00 bases by metal-induced hydrolysis prior to hybridization. Target hybridization was performed in an Affymetrix hybridization oven atEthics StatementAll animal protocols were approved by the Fox Chase Cancer Center IACUC (BIBS39 price protocol #05-06) and done in compliance with NIH guidelines. Animals were monitored daily for signs of distress and suffering. If distress or tumors were detected, animals were euthanized by overdose with isoflurane.ImmunohistochemistryAutopsied materials were fixed in buffered formalin, embedded in paraffin, and processed as previously described [23]. Rat antibodies directed against mouse CD45R/B220 (BD Biosciences)Mtap 23148522 Accelerates Tumorigenesis in Mice45uC for 16 hours using an Affymetrix GeneChip Mouse Genome 430A 2.0 Array. After hybridization arrays were washed using the Affymetrix fluidics station and AN 3199 site stained with streptavidin Phycoerythrin according to the Affymetrix protocol. Four bacterial and phage cRNA controls (BioB, Bio C, Bio D and Cre) were included in the hybridization buffer to serve as internal control for hybridization efficiency. Washed arrays were scanned on an Affymetrix GeneChip Scanner 3000. Data was normalized using RMA as previously described [35]. Array data can be accessed in the GEO repository, GSE44539.Pathway AnalysisFor pathway analysis, we selected a set of differentially regulated genes based on the criteria that they exhibited at least a 50 change in mRNA levels and had a p-value ,0.01 (FDR ,0.29). This list, containing 363 probes, was then analyzed using both Web Gestalt Gene Analysis Toolkit V2 [36], and the Ingenuity Pathways Analysis software (IPA, Ingenuity Systems, http://www. ingenuity.com). Both the Web Gestalt and IPA software maps the enriched genes on various canonical pathways and determines if the number of hits in each pathway exceeds those estimated by chance. The Web Gestalt software gives both an unadjusted and an adjusted P-value, where the adju.Re the deceased animal was relatively fresh, necropsies were performed to determine if tumor was present at time of death. In cases where a tumor could not be confirmed at the time of necropsy, animals were censored for the purposes of survival analysis.Mtap QuantificationMtap protein levels were detected by Western blot analysis using a MTAP monoclonal antibody (Santa Cruz Biotechnology) at a 1/1000 dilution. Signal was visualized by SuperSignal West Pico Chemiluminescent kit (Pierce), and signal was quantified using Alpha Innotech image analyzer. All levels were normalized to an alpha-actin internal control. Mtap expression ,20 that of control samples was scored as Mtap2.Microarray ExperimentsLivers from 100-day-old male Mtap+/+ and MtaplacZ/+ mice were excised and put into RNAlater (Ambion). Total RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA) and further purified by RNeasy kit (Qiagen, Valencia, CA) according to manufacturer’s instructions. RNA quality was evaluated by electrophoresis on Agilent Bioanalyzer (Agilent). Five mg of total RNA was first transcribed into cDNA using the Invitrogen’s Superscript system with an oligo (dT)24 primer containing a T7 RNA polymerase promoter sequence at its 59 end. After double stranded cDNA synthesis using DNA polymerase I, Biotin-labeled cRNA was generated by in 16985061 vitro transcription using a GeneChip IVT Labeling Kit (Affymetrix) according to manufacturer’s instructions and then purified using the GeneChip Cleanup Module. Label target was fragmented to a size of 35?00 bases by metal-induced hydrolysis prior to hybridization. Target hybridization was performed in an Affymetrix hybridization oven atEthics StatementAll animal protocols were approved by the Fox Chase Cancer Center IACUC (Protocol #05-06) and done in compliance with NIH guidelines. Animals were monitored daily for signs of distress and suffering. If distress or tumors were detected, animals were euthanized by overdose with isoflurane.ImmunohistochemistryAutopsied materials were fixed in buffered formalin, embedded in paraffin, and processed as previously described [23]. Rat antibodies directed against mouse CD45R/B220 (BD Biosciences)Mtap 23148522 Accelerates Tumorigenesis in Mice45uC for 16 hours using an Affymetrix GeneChip Mouse Genome 430A 2.0 Array. After hybridization arrays were washed using the Affymetrix fluidics station and stained with streptavidin Phycoerythrin according to the Affymetrix protocol. Four bacterial and phage cRNA controls (BioB, Bio C, Bio D and Cre) were included in the hybridization buffer to serve as internal control for hybridization efficiency. Washed arrays were scanned on an Affymetrix GeneChip Scanner 3000. Data was normalized using RMA as previously described [35]. Array data can be accessed in the GEO repository, GSE44539.Pathway AnalysisFor pathway analysis, we selected a set of differentially regulated genes based on the criteria that they exhibited at least a 50 change in mRNA levels and had a p-value ,0.01 (FDR ,0.29). This list, containing 363 probes, was then analyzed using both Web Gestalt Gene Analysis Toolkit V2 [36], and the Ingenuity Pathways Analysis software (IPA, Ingenuity Systems, http://www. ingenuity.com). Both the Web Gestalt and IPA software maps the enriched genes on various canonical pathways and determines if the number of hits in each pathway exceeds those estimated by chance. The Web Gestalt software gives both an unadjusted and an adjusted P-value, where the adju.

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