Analysis of Zika Virus gene expression by Ribosome profiling and RNA sequencing
ABSTRACT: Ribosome profiling (Ribo-Seq) (maps positions of translating ribosomes on the transcriptome) and RNA-Seq (quantifies the transcriptome) analysis of African green monkey (Vero E6) cells and Aedes albopictus (C6/36) cells infected with Zika Virus (ZIKV) strain PE243. Cells were harvested at 24 h post infection (p.i.) and Ribo-Seq and RNA-Seq libraries were prepared and deep sequenced.
Project description:Ribosome profiling (Ribo-Seq) (maps positions of translating ribosomes on the transcriptome) and RNA-Seq (quantifies the transcriptome) analysis of chicken (Gallus gallus) cells infected with Infectious Bronchitis Virus (IBV) strains Beaudette and M41.
Project description:Ribosome profiling (Ribo-Seq) (maps positions of translating ribosomes on the transcriptome) and RNA-Seq (quantifies the transcriptome) analysis of Rattus norvegicus cells infected with Moloney Murine Leukemia Virus (Mo-MuLV).
Project description:The effects of RyhB expression were examined by Ribo-seq and RNA-seq after 10 min to avoid indirect effects. Expression of RyhB was induced by arabinose from cells carrying pBAD-ryhB plasmid. The RyhB expression was confirmed by real-time PCR. As a control, cells with vector pNM12 were grown and induced. The cells were pulverized and total mRNAs were extracted from the pulverized cells and processed for Ribo-seq and RNA-seq.
Project description:Ribosome profiling (RiboSeq) (maps positions of translating ribosomes on the transcriptome) and RNASeq (quantifies the transcriptome) analysis of murine 17 clone 1 (17Cl-1) cells infected with Murine coronavirus strain A59 (MHV-A59). Samples comprise 1 and 8 h mocks, 1, 2.5, 5 and 8 h post infection timecourse, for each of RiboSeq with cycloheximide (CHX), RiboSeq with harringtonine (HAR), and RNASeq, performed in duplicate (6 x 3 x 2 libraries); RiboSeq CHX, RiboSeq HAR and RNASeq at 1 h post infection for high multiplicity of infection (3 libraries); and 1 long-read library for 5 h post infection RiboSeq CHX to test for larger-than-normal ribosome footprints.
Project description:Ribosome profiling (Ribo-Seq) and RNA-Seq analysis of eEF3 depletion in yeast (Saccharomyces cerevisiae). eEF3 depletion was induced by methionine in a modified strain where the native promoter was replaced by methionine repressible MET25 promoter. Conditional depletion enables us to study global effects of an essential gene.
Project description:Methods: RNA-sequencing was performed on matched samples obtained across several different gene expression measurement methods including: (a) fresh-frozen (FF) RNA samples by mRNA-seq, Ribo-zero and DSN and (b) FFPE samples by Ribo-zero and DSN. We also assayed the matched samples with Agilent microarray. RNA-seq data was compared on the rRNA-removal efficiency, genome profile, library complexity, coverage uniformity and quantitative cosinstency across protocols and with microarray data. Results: Compared to mRNA-seq, Ribo-zero provides equivalent percentage of rRNA component, genome-based mapped reads, and consistent quantification of transcripts. Moreover, Ribo-zero and DSN protocols achieve concordant transcript profiling in FFPE samples, and provide substantially more information on non-poly(A) RNA, which cannot be captured by mRNA-seq. Therefore, our study provides evidence that RNA-sequencing can generate accurate and reproducible transcript quantification using FFPE tissues. mRNA profile of 11 breast tumors were assayed by Agilent microarray, and by RNA-sequencing on libraries including: (a) fresh-frozen (FF) RNA samples by mRNA-seq, Ribo-zero and DSN and (b) FFPE samples by Ribo-zero and DSN, using Illunia HiSeq2000 2x50bp. RNA-Seq raw data is to be made available through dbGaP (controlled access) due to patient privacy concerns: http://www.ncbi.nlm.nih.gov/gap/?term=phs000676