Transcriptional analysis of the early liver stage of Plasmodium falciparum parasites
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ABSTRACT: Determination of gene expression level changes of whole genome during Plasmodium falciparum development in early liver stage (at 24h and 48h), compared to mixed blood stage and sporozoite stage. A set of Genes selected from this expression analysis are further verified by qPCR and a sub-set were tested for their vaccine efficacy. 6 genomic tiling arrays: 3 time points in early liver infection (spz, hr24, hr48), and 3 blood stage isolates
Project description:Investigation of comprehensive gene expression level changes in male strobili of sterile mutant, compared to the fertile plant. We designed a new custum array derived from ESTs of Cryptomeria japonica for this study. Male strobili of C. japonica were collected from Toyama 1 half-sib F2 pedigree. Toyama 1 male-sterile mutant was first reported in Saito, M. , H. Taira, and Y. Furuta (Journal of Forest Research 3(3):167-173). Microarray studies using both individual samples and pooled samples were performed. Total RNA was extracted from male strobili at four developmental stages derived from each seven fertile and male-sterile trees as individual samples. Pooled RNA samples were prepared from four to eight different fertile and sterile plants at three developmental stages.
Project description:Hepatoarcinogenesis is a slow and multistep process. We used Hepatitis B virus X antigen (HBx) induced Hepatocellular carcinoma (HCC) as model. We also identify the biomarkers, the pathways and networks underlying HCC formation in this animal model. We analyzed the events from the early, middle, and late stages, in order to predict and prevent the development of cancer. At each specific stage, we analyzed the expression level that differed at least two-fold between HBx transgenic and wild-type mouse liver. Statistical approaches were used to identify genes displaying an increasing or decreasing trend throughout hepatocarcinogenesis. The liver was excised from 6-week-, 8-month-, 12-month-, 14-month-, and 16-month-old HBx transgenic mice (A106 strain) and RNA samples were isolated. In both 14-month- and 16-month-old mice, samples were obtained from both the tumor tissue and the normal.
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:The profiling was conducted with the Rice 3'-Tiling 135k Microarray designed from 31,439 genes deposited at IRGSP, RAP2 database (http://rapdb.lab.nig.ac.jp). In this research, an array of 31,439 rice genes was used to elucidate gene expression in leaf and panicles of non-transgenic and HMB4 over-expression line. The analyses show that transgenic rice induces early flowering due to an enhancement of stress response. A total of 20 chips were used for microarray. Total RNAs were extracted from rice leaf and panicle. Experiments were duplicated.
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 genome-wide gene expression in sepals, petals, stamens, staminodia and carpels in pre-anthesis Aquilegia flowers. One goal was to identify transcriptional signatures associated with petaloidy by comparing gene expression in petals and petaloid sepals. Other goals were to study the evolutionary origin and ecological function of staminodia by comparing a) expression patterns in stamens, staminodia and carpels, b) identifying transcriptional regulators expressed in staminodia and c) using gene set enrichment analysis to identify biological processes operating in staminodia. A 15 chip study using total RNA from the five floral tissues from three replicate natural populations with each sample representing tissue pooled from 60 flowers.
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.