We have identified candidate genes from the Feml2 QTL influencing femur length through allele specific expression analysis of growth plates in C57BL/6J x CAST/EiJ F1 hybrids. This work provides the foundation to identify novel genes affecting bone geometry. Overall design: total RNA sequencing in 7 male C57BL/6JxCAST F1s
Genetic Dissection of a QTL Affecting Bone Geometry.
Sex, Age, Specimen part, Cell line, Subject
View SamplesPurpose: To identify regulatory proteins that are potential drivers of a coordinated breast cancer metastasis gene expression signatures. Methods: Knockdown of target genes in breast cancer cell lines was achieved using scramble and/or gene-specific siRNA (ON-TARGET SMARTpool, Thermo Scientific) and Lipofectamine RNAiMAX. 48h post transfection, total RNA was isolated from cell lines using the RNeasy Plus mini prep kit (Qiagen). Nucleic acid quality was determined with the Agilent 2100 Bioanalyzer. RNA Sequencing was also performed at the New York Genome Center (Manhattan, NY, USA) using a HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina, San Diego, CA, USA). Results: Raw reads in the fastq format were aligned to Human Genome HG19 using the RNA-seq STAR aligner version 2.4.0d (http://www.ncbi.nlm.nih.gov/pubmed/23104886, http://www.ncbi.nlm.nih.gov/pubmed/26334920) as recommended by user manual downloaded along with the software. STAR aligner was chosen for mapping accuracy and speed (http://www.nature.com/nmeth/journal/v10/n12/full/nmeth.2722.html). Mapped reads for each sample were counted for each gene in annotation files in GTF format (gencode.v19.annotation.gtf available for download from GENECODE website (http://www.gencodegenes.org/releases/19.html)) using the FeatureCounts read summarization program (http://www.ncbi.nlm.nih.gov/pubmed/?term=24227677) following the user guide (http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf). Individual count files were merged to generate the raw-counts matrix by an in-house R script, normalized to account for differences in library size and the variance was stabilized by fitting the dispersion to a negative-binomial distribution as implemented in the DESeq R package (http://bioconductor.org/packages/release/bioc/html/DESeq.html)(Anders and Huber, 2010). Conclusions: Our data suggest that targeting keystone proteins in the breast cancer metastasis transcriptome can effectively collapse transcriptional hierarchies necessary for metastasis formation, thus representing a formidable cancer intervention strategy. Overall design: Examination of mRNA profiling of breast cancer cell lines after knock-down of putative master regulators of the breast cancer metastasis transcriptome
An Integrated Systems Biology Approach Identifies TRIM25 as a Key Determinant of Breast Cancer Metastasis.
Specimen part, Cell line, Subject
View SamplesExpression profiling of rapidly-induced genes upon VSV infection at 4 hours post-infection in Drosophila cells
Transcriptional pausing controls a rapid antiviral innate immune response in Drosophila.
Cell line
View SamplesTo determine the Cdk9 targets of VSV-induced genes in Drosophila cells at 4 hours post-infection
Transcriptional pausing controls a rapid antiviral innate immune response in Drosophila.
Cell line, Treatment
View SamplesmiR-92 enhances c-Myc induced apoptosis. In the R26MER/MER mouse embryonic fibroblasts (MEFs), a switchable variant of Myc, MycERT2, was knocked into the genomic region downstream of the constitutive Rosa26 promoter, allowing acute activation of c-Myc by 4-OHT-induced nuclear translocation. This in vitro system nicely recapitulates c-Myc-induced apoptosis, as activated MycERT2 induces strong p53-dependent apoptosis in response to serum starvation. Enforced miR-92 expression in three independent R26MER/MER MEF lines significantly enhanced Myc-induced apoptosis.
A component of the mir-17-92 polycistronic oncomir promotes oncogene-dependent apoptosis.
Specimen part
View SamplesThe circadian clock generates daily rhythms in mammalian liver processes, such as glucose and lipid homeostasis, xenobiotic metabolism, and regeneration. The mechanisms governing these rhythms are not well understood, particularly the distinct contributions of the cell-autonomous clock and central pacemaker to rhythmic liver physiology. Through microarray expression profiling in MMH-D3 hepatocytes, we identified over 1,000 transcripts that exhibit circadian oscillations, demonstrating that many rhythms can be driven by the cell-autonomous clock and that MMH-D3 is a valid circadian model system. The genes represented by these circadian transcripts displayed both co-phasic and anti-phasic organization within a protein-protein interaction network, suggesting the existence of competition for binding sites or partners by genes of disparate transcriptional phases. Multiple pathways displayed enrichment in MMH-D3 circadian transcripts, including the polyamine synthesis module of the glutathione metabolic pathway. The polyamine synthesis module, which is highly associated with cell proliferation and whose products are required for initiation of liver regeneration, includes enzymes whose transcripts exhibit circadian oscillations, such as ornithine decarboxylase (Odc1) and spermidine synthase (Srm). Metabolic profiling revealed that the enzymatic product of SRM, spermidine, cycles as well. Thus, the cell-autonomous hepatocyte clock can drive a significant amount of transcriptional rhythms and orchestrate physiologically relevant modules such as polyamine synthesis.
Cell-autonomous circadian clock of hepatocytes drives rhythms in transcription and polyamine synthesis.
Specimen part, Cell line
View SamplesThis SuperSeries is composed of the SubSeries listed below.
The exoribonuclease Nibbler controls 3' end processing of microRNAs in Drosophila.
Sex, Specimen part
View Samplesnbr/CG9247 gene function regulates the length of the 3'end of miRNAs.
The exoribonuclease Nibbler controls 3' end processing of microRNAs in Drosophila.
No sample metadata fields
View Samplesnbr/CG9247 gene regulates 3''end heterogeneity of a subset of miRNAs. It is not clear how broad this effect is on small RNA population. To address this, we compared small RNA population in wild-type and tmr[f02257] mutants. This approach identified more miRNAs whose 3''end heterogeneity was affected in nbr[f02257] mutants. Overall design: 2-3 day old control (w homogeneous strain Bloomington stock center 5905) and nbr[f02257] null mutant flies were collected. nbr[f02257] line was in the homogenous (Bloomington stock center stock 5905) background through a minimum of 5 backcrosses. Total RNA from whole flies was extracted using TRIzol reagent (Invitrogen). 40ug of total RNA from each genotype was used for small RNA library preparation with Small RNA Sample Prep kit (v1.5) (Illumina).
The exoribonuclease Nibbler controls 3' end processing of microRNAs in Drosophila.
Sex, Specimen part, Subject
View SamplesFrankincense oil is prepared from aromatic hardened wood resin obtained by tapping Boswellia trees. For thousands of years, it has been important both socially and economically as an ingredient in incense and perfumes. Frankincense oil is a botanical oil distillate made from fermented plants that contains boswellic acid, a component known to have anti-neoplastic properties. We evaluated frankincense oil-induced cytotoxicity in bladder cancer cells. With a window of concentration, frankincense oil suppressed cell viability and induced cytotoxicity in bladder transitional carcinoma J82 cells but not normal bladder urothelial UROtsa cells immortalized with SV40 large T antigen. However, frankincense oil-induced J82 cell death did not result in DNA fragmentation. Microarray and bioinformatics analysis confirmed that frankincense oil activated cell cycle arrest, suppressed cell proliferation, and activated apoptosis in J82 cells through a series of potential pathways. These finding suggest that bladder cancer can be treated through intravesical administration of pharmaceutical agents similar to direct application on melanoma.
Frankincense oil derived from Boswellia carteri induces tumor cell specific cytotoxicity.
No sample metadata fields
View Samples