Global transcriptome analysis in fast-growing Arabidopsis thaliana with elevated level of ATP [roots]
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ABSTRACT: Higher ATP supply in AtPAP2 overexpression line is the driving force for its fast-growth phenotypes, leading to massive changes in its transcriptome and metabolome. The OE lines are previously described in Sun et al., New Phytol. 2012 Apr;194(1):206-19. 20-day-old Arabidopsis seedlings at middle of day under long day growth conditions were collected for RNA extraction and microarray analysis
Project description:We performed RNA microarray in a low protein diet (LPD) model of IUGR at three key time points of alveolarization process. IUGR and control rat pups had been studied for each time point considered: on postnatal day 4 (P4) before beginning of the alveolarization process, on P10, peak of alveolarization process and on P21 at the end of it. A twelve chip study using total RNA extracted from 14 whole lungs intrauterine growth restricted rat pups compared to 15 controls. RNA was extracted at three key time points of alveolarization in postnatal life. RNA was pooled by groups of 2 ou 3 before analysis.
Project description:Investigation of whole genome gene expression level changes in patients treated with cyclophosphamide We have studied the gene expression profile for 11 patients with different types of hematological malignancies but all of them have been treated with CP i.v. Eleven patients were enrolled in this study. All of them were treated by i.v. infusion of CP 60 mg/kg/day once for 2 days followed by TBI. Blood samples were collected from each patient before the start of CP infusion, 6 h after CP first dose, before CP second dose (24 h after first dose) and 6 h after it.
Project description:Investigation on expression levels of normal tissue from prostate cancer patients on locus 8q24. The region chr8:127640000-129120000 is tiled with isothermal probes (hg17) 7 chip study, using 7 independent samples.
Project description:Investigation on expression levels of normal tissue from prostate cancer patients on locus 8q24. 3 chips with 3 arrays each study, using 3 pairs of normal vs. tumor tissue and 3 replicates of the same sample. Each chip contained one pair of normal vs. tumor and one copy of the repeated sample.
Project description:Investigation on expression levels of normal tissue from prostate cancer patients on locus 8q24. The region chr8:127640000-129120000 is tiled with 60 nt probes at 10 nt interval (hg18) 7 chip study, using 7 independent samples.
Project description:Higher ATP supply in AtPAP2 overexpression line is the driving force for its fast-growth phenotypes, leading to massive changes in its transcriptome and metabolome. The OE lines are previously described in Sun et al., New Phytol. 2012 Apr;194(1):206-19. 20-day-old Arabidopsis seedlings at middle of day under long day growth conditions were collected for RNA extraction and microarray analysis
Project description:Embryonic stem cells (ESCs) and induced-pluripotent stem cells (iPSCs) self-renew and differentiate into an array of cell types in vitro and in vivo. A complex network of genetic and epigenetic pathways regulates the self-renewal and differentiation of these pluripotent cells, and the structure and covalent modifications of chromatin play a prominent role in this process. We examine nucleosome occupancy in mouse and human embryonic stem cells (ESCs), induced-pluripotent stem cells (iPSCs), and differentiated cell types using MNase-seq. To address variability inherent in this technique, we developed a bioinformatic approach that enabled the identification of regions of difference (RoD) in nucleosome occupancy between pluripotent and somatic cells. The majority of changes in nucleosomal signatures that occur in differentiation are reset during reprogramming. We conclude that changes in nucleosome occupancy are a hallmark of pluripotency and likely identify key regulatory regions that play a role in determining cell identity. A six chip study using total RNA recovered from three cell types with 2 replicates each
Project description:Investigation of whole genome gene expression level changes of LncRNAs in tumor tissues and paired non-tumor tissues in HBV-positive hapatocellular carcinoma. The different expression genes were further analysised. The human LncRNA microarray analysis of the 10 samples (5 non-tumor tissues and 5 paired tumor tissues) were completed. Total RNA from each sample was quantified using the NanoDrop ND-1000 and RNA integrity was assessed using standard denaturing agarose gel electrophoresis. Total RNA of each sample was used for labeling and array hybridization as the following steps: 1) Reverse transcription with by Invitrogen Superscript ds-cDNA synthesis kit; 2) ds-cDNA labeling with NimbleGen one-color DNA labeling kit; 3) Array hybridization using the NimbleGen Hybridization System and followed by washing with the NimbleGen wash buffer kit; 4) Array scanning using the Agilent Scanner G2505C. Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and mRNA level (*_RMA.calls) files were generated after normalization. All mRNAs level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis.mRNAs that at least 3 out of 6 samples have values greater than or equal to lower cut-off: 50.0 (“All Targets Value”) were chosen for further data analysis. Differentially expressed mRNAs were identified through Volcano Plot filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable mRNAs expression pattern among samples.
Project description:A significant percentage of HIV-infected individuals experience a sharp decline in CD4+ T cell counts and progress to AIDS quickly after primary infection. Identification of biomarkers distinguishing rapid progressors (RPs) versus chronic progressors (CPs) is critical for early clinical intervention and could provide novel strategies to facilitate vaccine design and immune therapy. mRNA and miRNA expression profiles in the peripheral blood mononuclear cells (PBMCs) of RPs and CPs were investigated at 111±22 days (Mean±SD) of HIV infection. The association of mRNA and miRNA expression with disease progression was examined by receiver operating characteristic analysis and Kaplan-Meier survival analysis. Pathway enrichment analysis showed that genes with deregulated expression in RPs are primarily involved in apoptosis pathways. Furthermore, we found that 5 miRNAs (miR-31, -200c, -526a, -99a and -503) in RPs were significantly decreased compared to those in CPs (P<0.05). The decreased expression of these miRNAs was associated with rapid disease progression of HIV infection with a 94% predictive value as measured by the area under the curve. The upregulated predicted targets from the 5 signature miRNAs and all upregulated genes identified from mRNA microarray converged to the apoptosis pathway. Moreover, overexpression of miR-31 in primary human T cells promoted their survival. Our results have identified a distinct transcriptomic signature in PBMCs of RPs and provided novel insights to the pathogenesis of HIV infection. A cohort of primary HIV infected individuals with different disease outcome were enrolled in this study. We included 6 individuals with rapid disease progression (RP), seven with chronic disease progression (CP). The HIV infected individuals were never on therapy before the time of sample taken.