Tissue specific profiling of the human pathogen Schistosoma japonicum
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ABSTRACT: Key tissues of the adult female parasite involved in nutritional uptake and reproduction were examined using a novel gene discovery approach that combined laser microdissection microscopy and microarray analyses. Gastrodermis, vitelline glands and ovary were microdissected from unfixed, frozen sections of the Asian species, Schistosoma japonicum. Total RNA was isolated from the enriched tissue preparations and microarray analyses undertaken to generate tissue specific gene expression profiles. Single colour adult female schistosome laser microdissection microarray data with technical replicates in duplicate: Gastrodermis (gut); vitelline glands (vitelline); ovary; and whole section (control).
Project description:To define the differential gene regulation of adult Schistosoma japonicum in response to host insulin, we utilised a parasite microarray with 38,444 probes representing 19,222 genes. We cultured male and female adult worms were exposed to insulin and glucose; and then parasites were collected at three time-points. There were 1,437 probes (1101 genes) up or down regulated (±1.5 fold change) by insulin after 0.5, 3, 24 hours, with the majority, 712 probes (577 genes) and 623 probes (486 genes) were up-regulated at 24 hour of adding insulin in males and females respectively compared with the control (without insulin). Single colour microarray, insulin treated adult Schistosoma japonicum with technical replicates in duplicate: Separate male and female worms exposed to insulin at 0, 0.5, 3, 24 hours. This study includes 6 control samples for separate male and female worms cultured without insulin at 0, 0.5, 3, 24 hours.
Project description:We have examined the gene expression profile of the transformation of the blood fluke Schistosoma mansoni from the cercarial to schistosomula stages. Specifically cercariae were mechanically transformed and then cultured for 3 hours or 5 days, and then total RNA was isolated and microarray analysis performed. A second experiment compares the effect that the presence of red blood cell in the culturing conditions has over the 3 hour and 5 day periods have on the parasite. Agilent custom designed microarray was used. One colour experimental design. One biological replicate was labelled and then two technical replicates (hybridisations) performed for each sample. A total of 5 samples were examined, cercariae, 3 hrs +RBCs, 5 days + RBCs, 3 hrs â??RBCs and 5 days â?? RBCs.
Project description:Key tissues of the adult female parasite involved in nutritional uptake and reproduction were examined using a novel gene discovery approach that combined laser microdissection microscopy and microarray analyses. Gastrodermis, vitelline glands and ovary were microdissected from unfixed, frozen sections of the Asian species, Schistosoma japonicum. Total RNA was isolated from the enriched tissue preparations and microarray analyses undertaken to generate tissue specific gene expression profiles.
Project description:In the present study, a oligonucleotide microarray platform is used to compare expression profiles of beef cattle muscle in animals treated with either Dexamethazone (Dex) or Dexamethazone plus 17?-estradiol (Estr) administered at sub-therapeutic dosage, against untreated controls. Seventeen male beef cattle 15-18 months old, around 450 kg mean body weight were randomly allocated in three groups: 6 were untreated (group Ctrl), 5 were administered with dexamethazone via feed 0.75mg/head for 43 days (group D); the last 6 animals were administered via feed for 43 days with Dex (0.75mg/head) and intramuscularly (i.m.) for three times with 17?-oestradiol, 20mg/head, (group DE). Three additional control animals, matching in sex and age, collected in a previous experiment were included in the Ctrl group to increase sample size and to control for biological variation. For each sample, total RNA was extracted from a specific anterior limb muscle (biceps branchii). Data analysis demonstrates that the expression profiles were strongly affected by Dex treatment with hundreds of genes up-regulated with relevant fold-change, whereas the myostatin gene was significantly down-regulated. On the contrary, the administration of Dex-Estr reveals a weaker effect on gene expression. In this study, we analyzed the gene expression profiles of 20 anterior limb muscle samples, 9 collected from untreated controls, 5 collected from cattle treated with Dex and 6 from cattle treated with Dex+Estr using Agilent-015354 Bovine oligo microarray platform (20 arrays, no replicate) based on single-colour detection (Cyanine-3 only). Microarrays are scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides are scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software creates a unique ID for each pair of XDR scans and saves it to both scan image files. Feature Extraction 9.5 uses XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal
Project description:Two different early developmental stages of gilthead sea bream: i) larvae at 24 hours post-hatching ( Stage 1), and ii) larvae at 96 hours post-hatching (Stage 4), were used for gene expression analysis. For each stage, total RNA was extracted from five (5) independent biological replicates, each consisting of pools of approximately 40-50 larvae. Based on SAM analysis, 1518 genes were differentially expressed between the two stages with a FDR (False Discovery Rate) of 0.0. In this study, we analyzed the gene expression profiles of two early developmental stages of gilthead sea bream using Agilent-016251 Sparus aurata Oligo Microarray platform (10 arrays, no replicate) based on single-colour detection (Cyanine-3 only). Microarrays are scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides are scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software creates a unique ID for each pair of XDR scans and saves it to both scan image files. Feature Extraction 9.5 uses XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal .
Project description:Technical replicates, consisting of four independent hybridizations of the same labelled cRNA, were performed to determine array-to-array reproducibility. After normalization, correlation index between all replicates exceeded 98%. In this study, we analyzed reproducibility of Agilent-016251 Sparus aurata Oligo Microarray based on single-colour detection (Cyanine-3 only). A RNA sample, prepared mixing four different larval stages of gilthead sea bream, was labelled in according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol. The same labelled cRNA was used for four independent fragmentation reactions and then hybridized spanning all array positions of 4x44K platform. Microarrays are scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides are scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software creates a unique ID for each pair of XDR scans and saves it to both scan image files. Feature Extraction 9.5 uses XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended Background-Subtracted Signal.
Project description:The aim of this study was to identify genes that are regulated by ccm2 signaling with the zebrafish heart at around 72 hours post fertilization. In total, 4 samples based on cDNA from extracted cardiac tissue were analyzed: 2 samples of ccm2 m201 mutant embryos and 2 WT control samples.
Project description:Human endometrial glands from early, mid and late secretory phases were captured using laser microdissection, and analyzed to characterize the gene expression changes during the window of implantation.
Project description:We investigated marmoset gastrulation using SpaTial Embryo Profiling (STEP) to generate 3D-transcriptomes based on the physical location of samples within the implanted embryo. Samples were isolated from unfixed tissues using laser-capture-microdissection and subjected to single-cell full-lengths transcriptome profiling using a modified version of Smart-Seq2.
Project description:The aim of this study was to identify genes that are regulated by Bmp signaling with the zebrafish heart at the heart cone stage around 21-23 hours post fertilization. In total, 4 samples based on cDNA from extracted cardiac tissue were analyzed: 2 samples of Tg(hsp70l:bmp2b)fr13 transgenic embryos heatshocked at 18 hpf and 2 WT control samples.