How can I determine the expression of EBV-coded genes by RNA-Seq?

09 September 2013 0 10K Report

I am using RNA-Seq to determine the gene expression in human tumor samples. Is there any way to determine the expression of the Epstein Barr Virus (EBV) coded genes by looking at the Illumina RNA-Seq data?

Badges
Science topic

More Can Kucuk's questions See All

Do you recommend Ion PGM or Ion Proton for mutation or expression analysis?

I'd like to hear your opinions about mutation or mRNA expression analyses based on your recent experiences with Ion Torrent platforms. Which bioinformatics tools are available for data...

01 February 2015 4,602 1 View

Is it possible to perform whole exome sequencing with 500X average coverage?

I'd like to know whether it is technically possible to improve rare mutant detection frequency by increasing the depth of the sequencing to 500X for WES using illumina library preparation kits and...

01 February 2015 5,403 6 View

What are the critical factors to be considered when establishing a new proteomic-metabolic core lab?

How much lab space is needed on average? What type of lab equipment/room organization is needed to minimize any contamination issues? Which instruments are the most user friendly and mechanically...

10 November 2014 7,015 1 View

Is there any public depository to upload the global methylation results of human patient samples during manuscript submission?

Public database to deposit methylation data.

09 October 2013 3,403 2 View

Is there a problem with my RNA pellet?

Hello, I am currently having problems with RNA extraction. I am using mouse liver (C57BL6J), and I have extracted RNA from mouse liver before. Before this experiment, my final RNA pellets were...

11 August 2024 7,082 3 View

Can I base on reverse DNA sequences to perform alignment, convert to amino acids and GenBank submission?

I have reverse sequences (AB1 format), can I base on reverse DNA sequences to perform nucleotide alignment, convert nucleotides to amino acids and deposit the sequence in GenBank database?

11 August 2024 5,138 1 View

Strugglling with m6A dot blot any suugesstion ?

I have been doing the m6A dot blot for a while with no improvement, I am extracting the RNA, and I can see the dots although the three biological replicas give a different reading on the memberan...

10 August 2024 8,539 5 View

How to confirm the site-directed mutagenesis result without performing NGS?

I'm cloning a fragment of 3200 nts into plasmid. The cloning was successful, however, 02 amino acids were mutated. Now I want to fix these 02 aa by site-directed mutagenesis technique using...

08 August 2024 4,645 2 View

RNA Extraction Using Hot Borate Method No Longer Working?

I've been performing RNA extraction on cotton petiole tissue for a few months now using the method described in the following paper, a derivative of the typical hot borate method...

08 August 2024 9,882 2 View

Does Anyone have expertise in in vitro transcription and RNA pull down assay?

I am currently working on LncRNA; to know the lncRNA-protein interactions I want to do RNA pull down assay, so I need to design primers with T7 promoter. I need assistance in this regard.

07 August 2024 6,622 1 View

E.coli contamination in human RNA seq data ?

Recently, we observed that 99% of the sequences in our RNA-seq data corresponded to the E. coli genome. Despite multiple DNAse treatments after RNA extraction and ribosomal depletion, we were...

06 August 2024 807 3 View

RNA later for the preservation of RNA in fecal samples at room temperature for one day (37°C)?

I am planning to collect human fecal samples for metatranscriptomic analysis using MGI. These samples are from indigenous people living in a region with high temperatures. I will have access to a...

06 August 2024 1,367 3 View

Why did the authors extrapolate a phenotype that they experimentally proved in one bacterial strain across the whole genus of the organism?

I aim to be as skeptical as possible regarding whether a pair of orthologous genes results in the same phenotype in their different but related bacterial organisms under similar environmental...

05 August 2024 6,787 4 View

Why my colony PCR results of my recombinant bacterial not showing any results?

I am performing ligation of the plasmid and a target gene. The steps I have taken are: 1. Double digestion of the plasmid and target gene 2. Ligation of the plasmid with the target gene 3....

05 August 2024 2,570 3 View