Supporting data for 'Functional characterization of Epstein-Barr virus encoded RNA 2 in the pathogenesis of nasopharyngeal carcinoma'

   A. Filename: chapter 3 SHAPE-MaP      

      Short description:        

    This file includes the analysing code by shapemapper2 and the resulting structures of the SHAPE MaP experiments. This is the supporting data for chapter 3 in my thesis.

        

   B. Filename: chapter 4 RAP-MS       

      Short description:        

   This file contains the raw data of mass spectrometry done in CPOS and the excel file for the proteins pulled down by EBER1, EBER2 probes or negative control. The MS/MS reads are the number of    reads for each proteins in each samples. The experiment was done in triplicates.

        

   C. Filename: chapter 5 RNA-seq     

      Short description:

     These are the RNA seq differential genes and transcripts excel files for M81 EBER2 or B95-8 EBER2 overexpression in C17 NPC cell lines. This experiment was done in triplicates. The fold change reflects the expression levels of each gene compared to negative control, and the lower FDR, the more significant the differential expression is.

   D. Filename:  Dataset_RT-qPCR      

      Short description:

      All RT-qPCR raw data generated from Roche LightCycler 480. The raw data was further labeled and analyzed in excel. The enrichment of each RNA in RIP-qPCR results in Chapter 4  and the validation of RNAseq and other funcitonal tests in chapter5 were shown in this file.

   E. Filename:  Dataset_Western      

      Short description:

    All the  photos of ECL developed membrane for western blotting generated by AI680. The photos were then further labeled and analyzed in ImageJ.  The levels of the input as well as IP of proteins or truncated proteins for each RIP-qPCR experiments for chapter 4 and the cell fractionatio assay for chapter 5 were shown by western blotting.