How to check the expression of a gene using the sequence of that gene?

Question

[Biologist]

Hi,

Based on the mouse experiments I am interested in determine the expression of a lncRNA of my interest in human ovarian cancer patient samples. Ensembl also shows that 5 transcripts of this lncRNA, and one of the transcript seems to be present in humans at same chromosome position as mouse acc to BLAT results.

I have the sequence of this transcript which is around ~750 bp. Among this sequence there are few identical regions found in humans.

I have 25 human ovarian patient samples and I'm interested in assessing the expression of this specific lncRNA using that sequence in patient samples. I have fastq files for all the samples.

How can I check the expression of this specific lncRNA in patient samples using sequence? Do I need to use the whole sequence or only the identical regions sequence?

Answer 1

[flogin]

" Do I need to use the whole sequence or only the identical regions sequence?"

It depends, if you want check if that region is expressed, you can use only the sequence of 750 pb (mapping with BowTie2, for example), but, if you want to evaluate the expression levels, you need to make a whole genome analysis and look for the expression levels of the loci of your sequence of interest (using STAR, for example).