Exactly you got the point. I did analysed both the 12 samples at the same time with their replicate but I am not sure whether is appropriate to do that by comparing all the 12 samples or just the infected cell lines (EJ28Pi VS TCCSUPPi). When is the global transcriptome is applied in my context. Could it be when combinining all the 12 samples in the analysis or when combining only the infected cell lines?
Thank you.
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"Global Transcriptome Analysis" <- from where have you heard this term, and in which context? It explains very little about what you actually [may] want to do. So, please tell us what you actually want to do.
Thank you Dr. Kevin for your prompt response. I have heard this term in so many different papers including nature articles. Refer to the following links frontier publishers, ASM Journal of Bacteriology in ASM and the nature publisher Scientific Reports. In my case, I want to see the changes in gene expression due to persistent viral infection from the established persistently infected cell lines (EJ28Pi and TCCSUPPi). So, I initially analysed the cells differently e.g. EJ28Pi VS EJ28 (control), and TCCSUPPi VS TCCSUP(control). However, now I want to know in which context does the term global expression or global transcriptome expression is applied. Is it by comparing the transcripts expression of EJ28Pi versus TCCSUPPi or is by comparing the triplicate of both EJ28Pi VS EJ28 and TCCSUPPi VS TCCSUP together in a single analysis?
Thank you.
No problem, Professor babasaraki. Oh, I see, but they are just using that term in a very general way, in the manuscript title. It just means that they have data from the [assumed] entire / global transcriptome, which they used for their analyses. So, 'global transcriptome analysis' can relate to any type of analysis that is performed using data from the transcriptome.
You may take the advice from Ahill in their answer (see below).
Thank you Sir. I appreciated. I am just a PhD student not to talk of a Professorial cadre. Just want to get the meaning of what I am doing in the analysis.
Many PhD students have more talent and maturity than Full Professors. You will be fine.
Thank you dear Professor for the compliment and words of motivation.