Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are using transcriptome profiling (RNA-seq) to evaluate the effects of EBV infection or (and) EBV BART6-3p mimics on the global transcriptome of the BJAB cells. Methods: BJAB cells were transfected with negative control mimics or BART6-3p mimics for 48 h and then infected with EBV virons for 2h. RNAs were extracted by Trizol and sequenced by Solexa high-throughput sequencing service (Oebiotech, Shanghai, China). Data were extracted and normalized according to the manufacturer’s standard protocol. Results: Log-fold changes of up- or down-regulated mRNAs between the control and experiment group were selected with a significance threshold of p<0.05. There are 408 mRNAs were up-regulated and 263 were down-regulated in “EBV infection” group cells comparing to “Mock” group cells. There are 385 mRNAs were up-regulated and 246 were down-regulated in “EBV infection + Bart6-3p mimics” group cells comparing to “EBV infection + negative control mimics” group cells. Conclusions: Our study describes the global transciptome changes of BJAB cells induced by EBV infection or (and) EBV 6-3p mimics.
Project description:Cellular targets for most of EBV miRNAs are not known. In our study, we aimed at identifying genes that are regulated by individual EBV mature miRNA, particularly BART 18-5p We used microarrays to explore the global gene expression (particularly the downregulated genes) targeted by EBV miRNA mimics. Burkitt's lymphoma cell lines, BL2 and BJAB, were transfected with miRNA mimic control (MC) and EBV miRNA mimics BART 18-5p, 10 and 14* for 24 hour prior to RNA extraction and hybridization on Affymetrix human HGU133 plus 2.0 microarrays.
Project description:Purpose: Evaluation of the m6A modification of EBV and BJAB transcripts during EBV infection Methods: Human B lymphoma cell line BJAB was uninfected or infected with EBV for 24 hours. Total RNA from each sample were extracted. Intact mRNA was isolated from total RNA samples and then chemically fragmented to 100-nucleoside-long fragments. m6A methylated mRNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody (a part of the fragmented mRNAs was kept as input). Both m6A enriched mRNAs and input mRNAs were concentrated for RNA-seq library construction. Sequencing was performed using an Illumina HiSeq 4000. Results: EBV EBNA2 and BHRF1 transcripts were m6A modified and m6A modification of BJAB transcripts changed during EBV infection. Conclusions: Our study found that some EBV transcripts were m6A modified during EBV infection and EBV infection changed m6A modification profiles of BJAB transcripts.
Project description:BJAB cells were infected with pNL-SIN-CMV-AcGFP (see accession number GSE8867 for data) or pNL-SIN-CMV-AcGFP expressing KSHV miR-K1, miR-K12-11 or miR-K4-3p and sorted 48 hours after infection. 12 or 16 days after transduction, cytoplasmic RNA was harvested and gene expression analysis of independent BJAB cell pools was performed using Human Operon v3.0.2 arrays. Each sample was run against Universal Human Reference RNA, Stratagene. The samples listed here were processed in parallel to those with accession number GSE8867, which includes all matched control cell lines. 6 independent B cell pools each expressing KSHV miR-K1, miRK12-11, or miR-K4-3p are included. Matched controls include unmodified BJAB (3 arrays) and cells transducted with parental vector pNL-SIN-CMV-AcGFP (6 replicates).
Project description:Small RNA-Seq study comparing Epstein-Barr virus (EBV) infected BJAB-B1 cells to isogenic, but uninfected, BJAB cells. The goal was to deduce differentially expressed small ncRNAs both micro and non-micro (up to 200 nt) between the two cell lines to gain insights into EBV-associated deregulation of host small ncRNAs.
Project description:RAW264.7 mouse macrophages were transfected with negative control and miR-342-3p mimics and subjected to microarray analysis 18 hours after the transfection. We used microarray to obtain global mRNA expression data of negative control and miR-342-3p mimics-transfected RAW264.7 cells.
Project description:BJAB cells were infected with pNL-SIN-CMV-AcGFP (see accession number GSE8867 for data) or pNL-SIN-CMV-AcGFP expressing KSHV miR-K1, miR-K12-11 or miR-K4-3p and sorted 48 hours after infection. 12 or 16 days after transduction, cytoplasmic RNA was harvested and gene expression analysis of independent BJAB cell pools was performed using Human Operon v3.0.2 arrays. Each sample was run against Universal Human Reference RNA, Stratagene. The samples listed here were processed in parallel to those with accession number GSE8867, which includes all matched control cell lines.
Project description:Analysis of gene expression change in U2OS cells expression synthetic miR-542-3p mimics. Forty-eight hours after transfection with negative miRNA mimics or miR-542-3p mimics, U2OS cells were subjected to RNA isolation.
