Project description:Here we describe CapTrap-Seq, an experimental workflow designed to address the problem of reduced transcript end detection by long-read RNA sequencing methods, especially at the 5' ends. We apply CapTrap-Seq to profile transcriptomes of the human heart and brain and we compared the obtained results with other library preparation approaches. CapTrap-Seq is a platform-agnostic method and here tested the method by using 3 different long-read sequencing platforms: MinION (ONT), Sequel (PacBaio) and Sequel II (PacBio).
Project description:Infectious bursal disease virus (IBDV) is the pathogenic agent of infectious bursal disease (IBD). Scine it was observed in 1957, IBD spread worldwidely in the chicken flocks, is a important immunosuppressive disease and an threat to poultry industry. Although many studies have be done about IBDV, interaction of IBDV infection and IBDV-encoding genes to host cell gene expression are little known. In this study, the LongSAGE library of Vero-cell, IBDV- infected vero cell, Vero-cell transfected with IBDV-VP5 gene, Vero-cell transfected with IBDV A frament and Vero-cell transfected with IBDV VP243 frament were obtained. We got 96,213 gene tags (17 nucleotides), which represented 24,475 transcripts. Keywords: Transcripts of different state vero-cell 1.Cloning of the full-length genomic A-segment, VP5 ORF cDNA, VP243 ORF cDNA of IBDV 2.Establishing cloned Vero cell lines expressing VP5, VP243 and A fragment of IBDV 3.Construction of Long-SAGE libraries 4. Sequencing
Project description:Clear cell renal cell carcinoma (ccRCC) is the most common form of kidney cancer. To date, long-read RNA sequencing has not been applied to kidney cancer. Here, we used ONT long-read Direct RNA sequencing to profile the transcriptomes of ccRCC cell line RCC4, with and without exposure to pro-inflammatory cytokines. Our results revealed differentially expressed genes induced by the pro-inflammatory cytokines. Moreover, results here revealed potential tumour origin of novel isoforms and genes that were discovered in the archival tumour samples by long-read sequencing.
Project description:Infectious bursal disease virus (IBDV) is the pathogenic agent of infectious bursal disease (IBD). Scine it was observed in 1957, IBD spread worldwidely in the chicken flocks, is a important immunosuppressive disease and an threat to poultry industry. Although many studies have be done about IBDV, interaction of IBDV infection and IBDV-encoding genes to host cell gene expression are little known. In this study, the LongSAGE library of Vero-cell, IBDV- infected vero cell, Vero-cell transfected with IBDV-VP5 gene, Vero-cell transfected with IBDV A frament and Vero-cell transfected with IBDV VP243 frament were obtained. We got 96,213 gene tags (17 nucleotides), which represented 24,475 transcripts. Keywords: Transcripts of different state vero-cell
Project description:This study reports a screen to identify putative inhibitors of the eIF4F complex for potential effects on blocking coronavirus replication, using HCoV-OC43 (OC43) infection of Vero E6 cells and the lung epithelial cancer line A549 as models.
Project description:To compare MicroRNA expression in Vero cells infected with DENV-2 adapted strain of Vero cells and its source srain derived from C6/36 cells
Project description:The LRGASP challenge encompasses different human, mouse, and manatee samples sequenced using multiple combinations of protocols and platforms. Different challenges will use distinct subsets of the samples for evaluation. The long-read sequencing platforms used in these challenges are the Pacific Biosciences (PacBio) Sequel II, Oxford Nanopore (ONT) MinION and PromethION. Samples will also be sequenced on the Illumina HiSeq 2500. The primary LRGASP library prep protocols are “standard” cDNA sequencing, direct RNA sequencing, R2C2, and CapTrap. Each sample will also include Lexogen SIRV-Set 4 spike-ins. We will also provide simulated PacBio and ONT data as part of the evaluations. This particular study focuses on single strand CAGE sequencing of human iPSCs, defining CAGE peaks from Illumina HiSeq 2500 (SR: 150 cycles) of two biological replicates for use in the LRGASP challenge.
Project description:The general aim of this paper is to explore a little further into molecular biology of the interaction between virus and host cell. We seek to use cDNA microarray technology, one revolutionary methodological advance, to perform a high throughput analysis of cDNA clones with the intent of identifying genes expressed in association with the infection with BKV in Vero cells (green monkey kidney cells). This technology, which can supply quantitative expression information for many thousands of genes simultaneously, has been used to classify the cellular genes at transcript levels in different physiological states of a tissue or cell. Accordingly, in this study, we have constructed a cDNA microarray containing 32448 spots (quadruplication of 7,334 human cDNAs and doping controls) to study that BKV infection of Vero cells. Our purposes were (i) to appraise whether cDNA microarrays could be employed to investigate the expression of cellular genes during the 5 time courses (5, 10, 15, 19 and 25 days post-infection (dpi)) of infection with BKV, (ii) to identify any genes that resulted in up-regulation or down-regulation of cell gene expression transcription, (iii) to determine the etiological role of BKV in nephropathy and/or neoplasia, (iv) to form a clearer picture of virus-associated pathophysiology in kidney. Keywords: BK virus, BKV, cDNA microarray, Vero cell We used a loop design in this study. cDNA microarray experiment consisted of ten RNA samples, including BKV-infected samples and their corresponding uninfected controls in 5 different time points. See supplementary PDF file for additional information