zika virus effect

Question

[sona]

How can I use RNA-seq data to find out differential gene expression in the HEK-293 cells?

[Ram]

How is this question different from your previous question?

Answer 1

[ATpoint]

You need RNA-seq of at least two groups, for example treated vs control. Each condition needs experimental replicates. Then you can use common tools for differential analysis sich as edgeR, limma and DESeq2. Read the manuals to get started.

[sona]

I have both the data but my objective is to find how it effects the neuronal cells, since HEK-293 cells have a neuronal marker .what protocol should I follow to achieve the objective?

[Ram]

how it effects

It cannot effect cells, it can only affect them.

[ATpoint]

There is no protocol to generate new insights. You need to know the literature on the topic and then interpret the differential expression results. Let your PI guide you. I find it questionable that an embryonic kidney cell line is suitable here, but experimental design and choice of model system is on you and your peers. You seem to be very new to all this. Be sure to get local guidance.