How would you compare the transcriptome of two cell types wi

How would you compare the transcriptome of two cell types with respect to whate genes are being expressed? Provide two possible approaches including both a general comparison and on that would identify specific genes.

Solution

To compare transcriptome of two cell types the possible approaches are:

1. DNA Microarrays: In this, small DNA spots of the particular cell will be placed on a chip/biochip. Expression level of genes present in both cell type samples can be measured. This technique is an old, long used technique. Nowadays, it has been replaced by RNA sequencing in many places.

2. RNA sequencing: In this technique, RNA produced by both the cell types would be sequenced. Only those RNAs will be present whose genes are expressed by the particular cell.

3. De novo transcriptome assembly: In this, transcriptome of both cell types will be created. The transcriptome will be created without the aid of reference genome. This method has many disadvantages. Structural alterations in RNA (which are created via splicing) are not considered here.