In order to understand the effect of genetic background on the response to gene dose perturbation, we performed mRNA transcriptional profiling on 99 hemizygotic lines (Df/+) from the DrosDel project, which have hybrid genetic background of OregonR/w1118. Overall design: We performed RNA-Seq analysis of 417 single adult flies in duplicate or triplicate. Flies are from 73 different genotypes. Differential gene expression was analyzed separately for each sex, gene expression from each genotype was compared to normalized mean of gene expression remaining 72 genotypes.
Dosage-Dependent Expression Variation Suppressed on the <i>Drosophila</i> Male <i>X</i> Chromosome.
Sex, Subject
View SamplesWe performed mRNA transcriptional profiling on 99 hemizygotic lines (Df/+) from the DrosDel project covering 68% of chromosome 2L, in order to understand how changes in gene copy number affect overall transcriptome. Overall design: We performed RNA-Seq analysis on 396 pools of 15-25 adult flies each. Samples include males or females from 99 different genotypes in duplicate. Differential gene expression was analyzed separately for each sex, by comparing each genotype with the remaining 98.
Dosage-Dependent Expression Variation Suppressed on the <i>Drosophila</i> Male <i>X</i> Chromosome.
Sex, Specimen part, Subject
View SamplesTo measure the response to gene dose, we performed mRNA-Seq of fly heads with molecularly defined deletions constructed from DrosDel deficiency lines (Ryder et al. Genetics 2007, 177(1):615-29) on the Illumina HiSeq 2000 platform. Overall design: We performed single-end next-generation sequencing (RNA-Seq) on poly-A+ RNA extracted from adult female and male heads in biological triplicate. Besides wildtype females (XX) and males (XY) that were heterozygous for deletions, we also sequenced females that were transformed into males (XX males) by using mutations in the sex determination gene transformer-2 (tra2). The original lines with deletions, including 22 deletions on the chromosome X and 12 deletions on the chromosome 3L, were from the DrosDel project. The diploid controls without DrosDel deletions were derived from w1118 (the parental line of DrosDel stocks) or Oregon-R Strain. We sequenced a total of 249 samples.
Dosage-Dependent Expression Variation Suppressed on the <i>Drosophila</i> Male <i>X</i> Chromosome.
Sex, Subject
View SamplesWe used RNA-seq to monitor mRNA levels of all genes in response to hypoxia of wild-type yeast, S. cerevisiae (strain yMH914 with wildtype HAP1). To gain insights into how gene expression changes over time, cells were subjected to 100% nitrogen gas and collected after 0,5,10,30,60,120,180, and 240 minutes. Total RNA was extracted and mRNAs were enriched by polyA selection. The cDNA was prepared into a sequencing library, multiplexed and single-end sequenced by an Illumina HiSeq 2500 sequencer. After mapping with Tophat2, the number of reads per feature was calculated using HTSeq. Overall design: RNA-seq analysis of eight time points of a yeast strain grown in hypoxia. There are three biological replicates of the time course.
Time-Course Analysis of Gene Expression During the Saccharomyces cerevisiae Hypoxic Response.
Subject
View SamplesVascular smooth muscle cells (VSMCs) respond to biomechanical stretch with specific changes in gene expression which govern the phenotype of these cells. The mechanotransducer zyxin is a
Loss of the mechanotransducer zyxin promotes a synthetic phenotype of vascular smooth muscle cells.
Specimen part, Treatment
View SamplesTo normalize transcriptome data we combined total RNA isolated from 10^6 resting or activated B cells with 1 µl of 1/10 dilution of Ambion’s ERCC RNA Spike-in Mix (92 mRNA standards). mRNA was then isolated and processed following Illumina’s RNA-seq protocol v2.
Global regulation of promoter melting in naive lymphocytes.
None
Specimen part, Cell line
View SamplesA chemopreventive effect of aspirin (ASA) on lung cancer risk is supported by epidemiologic and preclinical studies. We conducted a randomized, double-blind, placebo controlled study in current heavy smokers to compare modulating effects of intermittent versus continuous low dose ASA on gene signatures of smoking and lung cancer from nasal brushings. Fifty-four participants were randomized to intermittent ASA (ASA 81 mg daily for one week alternating with placebo daily for one week) or continuous ASA (81 mg daily) for 12 weeks. The primary endpoint was modulation of a smoking gene signature in nasal brushings. Other [JB1] endpoints included modulation of nasal and bronchial gene signatures for smoking, lung cancer and chronic obstructive pulmonary disease (COPD) and changes in cyclooxygenase (COX)- and 5-lipoxygenase (LOX)-mediated arachidonic acid (ARA) metabolism.
Effect of Intermittent Versus Continuous Low-Dose Aspirin on Nasal Epithelium Gene Expression in Current Smokers: A Randomized, Double-Blinded Trial.
Sex, Age, Subject, Time
View SamplesGlioblastoma multiforme is the most common and aggressive form of brain cancer. The use of oncolytic HSV-1 (oHSV) to selectively target brain cancer cells leading to their lytic destruction has shown to be very promising in a preclinical setting, but is lacking efficacy in clinical trials. Cyr61, a secreted extracellular matrix protein which functions to promote angiogenesis, migration, proliferation and tumorigenesis, was found to be upregulated rapidly following oHSV infection. Here we show, using microarray analysis, that Cyr61 expression leads to the induction of several genes with type 1 interferon function. We show that Cyr61 mediated type 1 IFN induction is through its interaction with integrin alpha6beta1 on the cell surface and results in oHSV inhibition, reducing the efficacy of this therapy.
Extracellular matrix protein CCN1 limits oncolytic efficacy in glioma.
Cell line
View SamplesThe aim of this study was to explore what molecular and cellular processes predicate the conversion from insulitis to diabetes. The transcriptional profiles of CD45+ immune cells collected from pancreas of a cohort of age-matched female mice, which were scanned by MRI to determine the risk of diabetes development.
Early window of diabetes determinism in NOD mice, dependent on the complement receptor CRIg, identified by noninvasive imaging.
Sex, Age, Specimen part
View SamplesGene expression was compared between E18.5 E-cadherin conditional knockout (cKO) small intestine and E18.5 control mouse small intestine.
E-cadherin is required for intestinal morphogenesis in the mouse.
Specimen part
View Samples