ABSTRACT: Impact of antibiotics (T2) or antibiotics in combination with stress (T3) in early life on intestinal functioning in pigs on 8, 55, 176 days in jejunum and ileum (blood only day 8) and control pigs (T1) 4 pools consisting of 16 animals were generated per time-point (day 8, 55, 176 after birth) per treatment (T1;control, T2; antibiotics, T3; antibiotics+stress)
Project description:Haploid (1N) and diploid (2N) Emiliania huxley (RCC 1217 and RCC1216) were grown in dilute batch culture and achieved stationary phase. We sampled two time points, at early (T2) and late (T3) stationary phase. Controls are haploid or diploid cells derived from dilute cultures (T1) growing in replete control medium. All samples were hybridized against a common, pooled baseline RNA. All experiments and hybridization were done in independent biological triplicates (A, B and C).
Project description:The aim of the current study was to characterize the genetic adaptive pathways altered by exercise in veteran athletes and age-matched untrained individuals. Two groups of 50-60 year old males: competitive cyclists and untrained, minimally active individuals were examined. All participants completed an acut bout of submaximal endurance exercise and blood samples pre- and post-exercise were analyzed for gene expression changes utilizing genome-wide DNA microarray analysis. Our results indicate distinct differences in gene expression involving energy metabolism, lipids, insuling signaling and cardiovascular function between the two groups. These findings may lead to new insights into beneficial signaling pathways of healthy aging and help identify surrogate markers for monitoring exercise and training load. Blood samples from the control and athlete groups were analyzed at three time-points: T1 (before exercise); T2 (immediately after exercise) and T3 (24 hours after exercise). There were n = 4 samples in each of control and athlete group at T1 and T3; and n = 7 for control group and n = 8 for athlete group at T2. One athlete sample (Sample # 010201) at time - point T2 had a technical replicate.
Project description:In order to test the gene expression profile in postinflammatory hyperpigmentation, micoarray studies were performed. Totally 14 subjects ( 7 at each phase) were treated by suction blister, and samples from treated area and corresponding control area ( from the same subjects) were taken at 1 week(t1), 2 weeks(t2), 4 weeks(t3), 6 weeks(t4), and 16 weeks(t5) after treatment. Paired samples from subject 6382 at 6th week were missing for microarray hybridization. Therefore, there are 138 array chips available for statistical analysis.
Project description:We have witnessed the rise and fall of antiangiogenic therapy in breast cancer (BC). Nevertheless, clinical remissions were observed in patients and we were interested in studying the activity of antiangiogenic drugs in BC. Inefficacy of sunitinib was observed in mouse models of metastatic BC, where evidence of enhanced metastasis was reported, and lack of efficacy of sunitinib-docetaxel combination was recently reported in a phase III clinical trial. Our aim was to understand the mechanisms and predictors of response to sunitinib in BC in a cohort of patients with untreated locally advanced or operable BC treated with an upfront window of single agent sunitinib, followed by the combination of sunitinib and docetaxel. We have used microarray profiing to monitor the transcriptional changes associated with three distinct stages of treatment: at diagnosis and prior to any treatment (t1), after an upfront window of single agent sunitinib (t2) and after the combined treatment of sunitinib and docetaxel (t3). In addtion, this microarray data also allowed us to observe the transcriptional changes associated with primary resistance to angiogenic therapy in 4 of 12 patients likely mediated by an adaptive transcriptional response to hypoxia in these resistant tumors. In BC patients this is the first demonstration of primary resistance to antiangiogenic therapy. Overall design: Breast cancer samples were colected from human patients (n=8) for RNA extraction and hybridization on Affymetrix microarrays. Expression profiling on tumor material collected at the three timepoints, diagnosis and prior to any treatment (t1), after an upfront window of single agent Sunitinib (t2) and after the combined treatment of sunitinib and docetaxel (t3), was used to obtain an unbiased view of sunitinib response. Several tumor biopsies and specimens had no frozen sample available or RNA with insufficient quality for expression analysis. Were include in the analysis, at diagnosis (t1), replicated material from patients 4, 5, 6, 7 and 11 (patient 10 had no replica), at day 15 (t2) replicated material from patients 5, 7, 11 and 12 (patient 4 had no replica) and at surgery (t3) replicated material from patients 7, 9, 10, 11 and 12 (patient 6 had no replica)
Project description:Total RNA extracted from differentiated mesenchymal stem cells at four time points (T1,T2,T3,T4) and sequenced using Illumina Hi-seq 2000 platform to generate RNA sequencing with 101bp in read length. Nearly 50 million raw reads were yielded from each sample respectively. We used FastQC to confirm the quality of raw fastq sequencing data, and SOAPfuse software to detect fusion transcripts. Discovering fusion genes from muscle differentiated mesenchymal stem cells
Project description:Genome-wide transcriptional analysis was performed on E. coli K12 exposed to 1 mg/ml of olive vegetation water phenolic extract (OVWPE) in planktonic condition. Three groups of samples were considered: P group (three replicate cultures with OVWPE extract diluted in ethanol 20%), E group (three replicate cultures with ethanol 20% alone) C group (three control replicate cultures). 1 ml of VWPE extract (1 mg/ml), 1 ml of ethanol 20% and 1 ml of LB broth were added respectively to the three groups when the OD600 of each culture reached 0.4. Cultures were sampled (2 ml) at the time of treatment (t1), 20 (t2) and 40 (t3) minutes after treatment.
Project description:A microarray targeting four sequenced strains in the Dehalococcoides (Dhc) genus was used to analyze gene expression in a robust long-term trichloroethene (TCE)-degrading microbial community (designated ANAS) during feeding cycles that involve conditions of periodic substrate supply. The Dhc transcriptome was examined at three time-points throughout a batch feeding cycle: T1 (27 h) when TCE, dichloroethene (DCE), and vinyl chloride (VC) were present; T2 (54 h) when only VC remained; and T3 (13 d) when Dhc had been starved of substrate for nine days. 90% of the Dhc ORFs that were detected in the ANAS DNA were found to be expressed as RNA sometime during the time course, demonstrating extraordinary utilization of the streamlined genome. 97% of these transcripts were differentially expressed during the time course, indicating efficiency of transcription through regulation in Dhc. Most Dhc genes were significantly down-regulated at T3, responding to a lack of substrate as would be expected. The tceA and vcrA genes, which code for proteins with known chlorinated ethene reduction functions, were highly expressed at both T1 and T2, whereas two other putative reductive dehalogenase genes (DET0173 and DET1545) were most highly expressed at T2, likely in response to the presence of VC. Hydrogenases were most highly expressed at T1, reflecting their important role in accumulating electrons used to initiate reductive dechlorination and other biosynthesis pathways. Cobalamin transport genes were preferentially expressed at T2, reflecting an increase in corrinoid transport as chloroethenes were degraded and a decrease in activity of the transport system after dehalogenation was complete. This is the first application of a microarray targeting a known genus, including both core genomes and identified strain-specific genes, applied to improve our understanding of transcriptional dynamics within an undefined microbial community. Replicate samples were independently collected, and simultaneously but individually extracted, fragmented, labeled, and hybridized to arrays. Three DNA samples (one from each of the three replicate cycles) and nine RNA samples (one from each of the three time-points in each of the three replicate cycles) were prepared for microarray analysis.
Project description:The study outcome was to evaluate the effect of the time on tumor samples and possibly select specific genes whose expression is time-related, that could be used as detectors of tissue degradation. RNA extracted from specimens of 14 patients at four time points after surgery was analyzed for gene expression on high-density oligonucleotide microarrays. A mixed-effects model implemented by considering the factor time (T0, T1, T2, T3) as fixed and the factor patient as random was used to identify probes with different expression means across the four different time points. The p-values of the model were adjusted with the Bonferroni method (p<0. 05).
Project description:The study outcome was to evaluate the effect of the time on normal colon mucosa samples and possibly select specific genes whose expression is time-related, that could be used as detectors of tissue degradation. RNA extracted from specimens of 15 patients at four time points after surgery was analyzed for gene expression on high-density oligonucleotide microarrays. A mixed-effects model implemented by considering the factor time (T0, T1, T2, T3) as fixed and the factor patient as random was used to identify probes with different expression means across the four different time points. The p-values of the model were adjusted with the Bonferroni method (p<0. 05).
Project description:Monocytes play a central role in the inflammatory response that follows acute myocardial infarction (MI). In order to study phenotypic adaptation of this cell type, we investigated patterns of monocyte gene expression in circulating monocytes at various stages of MI. Circulating monocytes were isolated from venous blood of MI patients at three time points: t1: within 6 hours after onset of chest pain (acute phase), t2: 3 days after MI (subacute phase), t3: 90 days after MI (chronic phase). For comparison, we studied a control group (n=21, data to be submitted later) with stable coronary artery disease. Using this transcriptomic analysis, we aimed to provide a more comprehensive reference of monocyte biology following acute MI and to aid in the identification of novel pathways and genes influencing the course of MI. Overall design: Monocytes play a central role in the inflammatory response that follows acute myocardial infarction (MI). In order to study phenotypic adaptation of this cell type, we investigated patterns of monocyte gene expression in circulating monocytes at various stages of MI. Circulating monocytes were isolated from venous blood of MI patients at three time points: t1: within 6 hours after onset of chest pain (acute phase), t2: 3 days after MI (subacute phase), t3: 90 days after MI (chronic phase). For comparison, we studied a control group (n=21, data to be submitted later) with stable coronary artery disease. Illumina Ref-8 v3.0 microarray arrays were used for whole-genome transcriptional profiling.