Comparing two RNAseq exepriments

[joxcargator73]

I am trying to compare significant expressed genes from two experiments.
Basically I have this:
Experiment 1: (Paired-end RNAseq)
Control(bacteria in Minimal medium) (3 replicates)
treatment1(bacteria with carbon source A) (3 replicates)
treatment2 (bacteria with carbon source B) 3 replicates)

Experiment 2: (Single-end RNASeq)
Control(bacteria in Minimal medium) (3 replicates)
treatment1(bacteria with carbon source C) (3 replicates)
treatment2 (bacteria with carbon source D) 3 replicates)

I conduct a first analysis of each experiment independently using DESeq and found the significant differential expressed genes.
Now I wonder if there is a way to compare results from experiment 1 and 2 and avoid bias of batch effects.
Can I analyzed exepriment1 and 2 together and correct for batch effect?
or Can I just take experiment 1 and 2 separately as independent experiments and contrast the significant expressed genes in each case?.

Thanks