Project description:Total RNA was collected from DU145-control(scr) and DU145-miR-106a transfected cells. Gene expression analysis was performed by The Centre for Applied Genomics (The Hospital for Sick Children, Toronto, Canada) using Affymetrix GeneChip Human Gene 2.0 ST array. Data were normalized using the default parameters in Affymetrix Expression Console Software 1.4. Genes downregulated 0.8-fold in miR-106a compared to control(scr) were identified as possible mRNA targets.
Project description:After extraction with mild non-denaturing detergents, we affinity-purified 785 endogenously-tagged CEPs and then identified stably-associated polypeptides by precision mass spectrometry. The resulting high-quality physical interaction network, comprising most (77%) of all targeted CEPs, revealed hundreds of previously unknown heteromeric complexes. Lab Heads: Andrew Emili; andrew.emili@utoronto.ca ;Donnelly CCBR, University of Toronto, Toronto ON M5S 3E1, Canada Mohan Babu; mohan.babu@uregina.ca ;Research and Innovation Centre, University of Regina, SK S4S OA2, Canada
Project description:Genome-wide DNA methylation profiling of MDA-MB-231 tumours with or without MTHFD2 knockdown and decitabine treatment. The Illimuna Infinium MethylationEPIC DNA Beadchip v-1-0 B3 was used to obtain DNA methylation performed by The Centre for Applied Genomics in Toronto, Canada.
Project description:Purpose: Next-generation sequencing (NGS) will be used to quantify whole transcriptome changes during genetic perturbations and viral infections Methods: RNA was harvested in Trizol 488 (Thermo Fisher). RNA was extracted using the manufacturer’s protocol and quantified by nanodrop. PANC1 wild-type or ARID1A knockout total RNA was sequenced by The Centre for Applied Genomics (TCAG) at The Hospital for Sick Children (Toronto, Canada) using the Illumina HiSeq2500 platform to generate single-end 100 bp reads. Adapters were trimmed using Trimmomatic and adapter-free reads were mapped to the human genome (hg19). Results: We have identified ARID1A KO to make cells more suceptible to viral infection due to decreased basal level of expression of ISGs Conclusions: Our study represents the first look at the role of ARID1A in the context of viral infection.
Project description:Ischemia reperfusion induced injury contributes to poor lung transplant outcomes.Microarrays were used to study the biological response of human lungs to the ischemia reperfusion process. Samples were collected from lung transplant cases at Toronto General Hospital. Lungs were donation after brain death (DBD)
Project description:This is a study indented to investigate the alterations in the molecular profile of cervix uteri, as it progresses thorough various FIGO stages of carcinoma, by means of global gene expression profiling, in a cohort of Indian patients. In addition expresion profiles of early and advanced stage cervical cancer were compared to identify biomarkers and therapeutic targets for the advanced stages. Cervical cancer and non-malignant cervical tissues are obtained from consenting patients following hospital ethics committee approved protocols. The samples are profiled against universal Human reference RNA from Stratagene on 19K EST microarrays from Microarray Center, University Health Network, Toronto, Canada. Biological replicates: Normal = 4; Cervical cancer Stage I = 8; Cervical cancer Stage II = 9; Cervical cancer Stage III = 8. One replicate per array.
Project description:Comparison of mouse ES cells and three different XEN cell cultures. Three XEN cell cultures: Two different strains (IM8A1 is PO, and XEN1-3 is ICR). And two different culture conditions (IM8A1-I versus IM8A1-II). Three biological replicates of XEN cell RNA were submitted to the Centre for Applied Genomics at the Hospital for Sick Children (Toronto, Canada) for preparation of cRNA and hybridization to the mouse U74Av2 Affymetrix gene array. QIAGEN RNeasy midi kit (QIAGEN Inc., Santa Clarita, CA) was used to extract total RNA from all samples according to manufacturer's instructions. The samples were (1) XEN1-3 cells at passage 18 (ICR strain, male) cultured on gelatin with 70% EMFI-CM, (2) IM8A1 cells at passage 27 (PO strain) cultured on gelatin with 70% EMFI-CM, (3) IM8A1 cells at passage 27 cultured on tissue culture plastic in RPMI 1640 (Gibco) supplemented with 20% FBS (CanSera, Rexdale, Canada), 1 mM sodium pyruvate, 2 mM L-glutamine, 50 mg/ml each of penicillin/streptomycin (all from Gibco), 100 uM b-mercaptoethanol (Sigma) for 4 days. RNA was also obtained from R1 ES cells grown in the absence of EMFIs in the above medium with LIF. Keywords = ES cells Keywords = XEN cells Keywords: ordered