making metadata file for differential gene expression analysis

Question

[Sara]

I have RNAseq data from patients from 2 time points (before and after treatment) and want to do gene expression analysis comparing 2 time points. if I want to use DESeq2, how should I make my metadata.csv file which will be used for differential gene expression analysis.

normally I make the metadata.csv file like this:

SampleID    Condition
patent1-1   T1
patent1-2   T2  
patent2-1   T1
patent2-2   T2  
patent3-1   T1
patent3-2   T2  
patent4-1   T1  
patent4-2   T2

and at the end I will get fold change and p-values. how I should make this file for my data to compare 2 time points? shall I do it per individual or include all patients in the same metadata.csv file?

[Basti]

You need to create a column patient, and then create a design ~ Patient + Condition