Project description:Arthropod-borne viruses (arboviruses) represent a threat to global public health, especially in the tropical and subtropical regions of the world. More than 150 arboviruses can infect humans; they cause mainly febrile illness, although hemorrhagic complications and diseases affecting the central nervous system (SNC) can also be observed. Arboviruses represent a threat to Brazil and, therefore, a permanent surveillance of these viruses is required to timely reduce the risk of epidemic outbreaks. The Brazilian Amazon region is where the highest number of arboviruses has been detected in the world. Besides, malaria is also endemic in the Amazon region, with a significant predominance of Plasmodium vivax. It is often difficult to differentiate between malaria and arboviral diseases, as they share similar clinical features and laboratory findings, mainly undifferentiated fever. This study aimed to estimate possible viral etiology in patients with febrile syndrome negative for Plasmodium infection, in the Brazilian Amazon. We initially analyzed serum samples of 124 participants with a DNA microarray platform designed for the detection of arboviruses and viruses transmitted by small mammals, but no virus was detected. Then, the serum samples of 76 participants were analyzed with a deep New Generation Sequencing, which showed evidence of the presence of only one arbovirus, the Zika virus in only one pool of 9 serum samples. This result is in contrast with our hypothesis, showing that arboviruses are not frequent in suspected malaria cases in Manaus, Brazil. Other viruses instead of arboviruses were found in this study. Primate erythrovirus 1 was the virus most frequently found virus in the suspected malaria patients, followed by Enterobacteria phage lambda. Besides, we detected, in a lower frequency, the Pegivirus C. In addition to the exogenous viruses, we also detected human endogenous retrovirus in all pools. Due to the high number of viruses that are important in the differential diagnosis of malaria, cost-effective and simple high throughput methods are required, helping molecular surveillance of misdiagnosed viral infections. Further studies with more robust sample sizes in other areas in the Amazon are needed.
Project description:we used next-generation sequencing technology to characterise mRNA-seq of brackish water (BW, 10‰), fresh water (FW, 0‰), and sea water (SW, 25‰)-treated Anguilla marmorata's gill, kidney and intestine to elucidate the molecular mechanisms of salinity adaptation.
Project description:We performed ChiP sequencing analysis for H3K27Me3 in DNA from mouse rib chondrocytes. Chromatin immunoprecipitation for H3K27Me3 in mouse rib chondrocytes after overnight culture.Chromatin Immunoprecipitation was performed using Cell Signaling Technology SimpleChIP Plus Enzymatic Chromatin IP Kit (Magnentic Beads) #9005 Sequencing using Next Generation Sequencing (Otogenetics), mapping of reads using DNA Nexus mapper and region calling using Quest software (DNA Nexus)
Project description:Next Generation Sequencing in cancer: a feasibility study in France to assess sample circuit and to perform analyzes within a limited time.
| 2274538 | ecrin-mdr-crc
Project description:Next generation sequencing of HBV RT Region
Project description:The transcriptome profiling of three samples in A. mongolicum Keng were studied using next-generation RNA sequencing under different drought stress conditions. This study aimed to identify genes of A. mongolicum Keng metabolism pathways that might be involved in this plant’s response to water deficit. 14.33 Gb high quality reads were assembled into 92,752 unigenes (unique transcripts), with a mean length of 1,303 bp. 76.26% had homologous genes in function databases.
Project description:In the process of searching for tumor-specific mutations to predict neoantigens for cancer immunotherapy in a Lynch Syndrome mouse model, tumorigenesis was induced with 1% DSS in drinking water. DNA was isolated from tumors and colon tissue separately from 4 MLH1-KO mice using the DNeasy Qiagen kit according to the manufacturer's protocol. Purity of the DNA was confirmed to be very high with the NanoDrop before sending samples to Illumina for next generation sequencing with the Agilent SureSelect XT Mouse All Exon kit. Finally, an analysis was performed in which common tumor-specific mutations were processed through in silico antigen prediction software in NetMHC.
Project description:Next generation sequencing was perfomed to identify differentially expressed micro-RNA in Placental tissue samples from IVF-ET assisted or natural conceived pregnancies
