Genome-wide expression profiles of primary human SAECs infected with different adenovirus mutants.
ABSTRACT: Full title: Genome-wide expression profiles of primary human small airway epithelial cells (SAECs) infected with different adenovirus mutants. Expression arrays were used to analyze global gene expression changes in SAECs infected with either mock, dE1B-55k, or d55k/dORF3 adenovirus at 36 hours post infection, as well as nutlin treatment for 12 hours. Overall design: Two independent experiments were performed with each experimental condition done in duplicate. CEL files were imported and analyzed with Partek Analysis software.
INSTRUMENT(S): [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [transcript (gene) version]
Project description:Full title: Genome-wide expression profiles of primary human small airway epithelial cells (SAECs) infected with different adenovirus mutants. Expression arrays were used to analyze global gene expression changes in SAECs infected with either mock, dE1B-55k, or d55k/dORF3 adenovirus at 36 hours post infection, as well as nutlin treatment for 12 hours. Two independent experiments were performed with each experimental condition done in duplicate. CEL files were imported and analyzed with Partek Analysis software.
Project description:Human Notch1 intracellular domain (NICD) was overexpressed in human primary lymphatic endothelial cells (LECs) for 10 and 24 hours by adenovirus. A GFP-control adenovirus-infected cells (24hours) and uninfected cells were also analysed as controls. Total RNAs were harvested and subjected to Affymetrix U133A microarray. Overall design: Human primary lymphatic endothelial cells (LECs) were isolated from human foreskin and cultured and expanded to population passages 5~6. Healthy subconfluent primary LECs were infected with adenovirus expressing human Notch1 intracellular domain (NICD) for 10 or 24 hours. In parallel, LECs were also infected with a GFP-expressing control adenovirus for 24 hours. Uninfected LECs were also used as a negative control in the same experiments *** CEL files unavailable/unrecoverable. ***
Project description:Adenovirus type 2 RNA splicing sites were mapped by using deep cDNA sequencing. The majority of the previously identified splice sites were detected. In addition, novel splicing sites were identified Total RNA obtained from four time stages of human primary lung fibroblast cells IMR-90 infected by adenovirus type 2 compared to the control mock-infected by adenovirus type 2.
Project description:We identified the abundance of isoforms of miRNAs encoded by human adenovirus 5 in total cytoplasmic RNA fractions of infected cells as well as in fractions containing the purified RNA-induced silencing complex (RISC). Overall design: Human A549 cells were infected with human adenovirus 5 at an MOI of 30 TCID50/cell or were mock-infected. Total RNA was isolated at 30h post-infection. In addition, RNA incorporated in RISC which was isolated by immunoprecipitation using an antibody recognizing all human Argonaute proteins was conducted as well. Purified RNAs were used to generate sRNA libraries with were subjected to RNA sequencing.
Project description:We sought to determine the effects of over-expression of Gli1 on gene expression in C2C12 myotube cultures. C2C12 myoblasts were induced to differentiate for 4 days. At that time, when >80% of nuclei were incorporated into multi-nucleated syncitial myotubes, we infected the cultures with recombinant adenovirus expressing GFP alone or GFP and a full length human Gli1. Media was changed 12 hours later. Cultures were lysed 60 hours after the initial infection. Gli1 over-expression induces de-differentiation of myotubes and proliferation of myoblasts. Results provide insight into the molecular basis of SHH signaling on skeletal muscle cells.
Project description:To compare the gene expression profile of MSCs harvested from bone marrow in the context of cell migration. Overall design: A total of 4 MSCs isolated from different donors were used. Duplicate samples were used for each hybridization. The experiment was repeated twice. CEL files obtained were imported into Partek Genomics suite for analysis. The final processed data were obtained from selecting for genes that have at least 2-fold difference in expression. The gene list was further narrow down to the keywords cell adhesion, chemokine, cytokine, and metalloproteinases.
Project description:We sought to characterize methylome remodeling during regional metastasis. We profiled the DNA methylome (n=44) and transcriptome (n=36) of matched primary breast tumors and regional metastases. Overall design: All paired samples (n = 88) were obtained following surgical resection at the MSKCC as part of routine clinical care, and snap frozen. Tumors were obtained in accordance with Institutional Review Board policies at the MSKCC. Each sample was examined histologically by a breast pathologist and microdissected to achieve >70% tumor cell content. Genomic DNA or RNA was extracted using the DNeasy kit (Qiagen) or RNeasy Kit (Qiagen) as per the manufacturer’s instructions. Expression analysis of tumors was performed using the Affymetrics U133 2.0 microarray (Affymetrix). Affymetrix CEL files were imported into the Partek Genomics Suite 6.1 (Partek), using RMA normalization.