Entering edit mode
4.8 years ago
gradstudentNew
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50
Hi there,
I recently conducted an experiment where I deleted a region of the genome. I found that there was a weird trend where the homozygous deletion for certain genes had higher expression compared to wild type, heterozygous deletion as shown below. I was wondering what your thoughts on this may be? I find it a bit weird that several genes within this region seem to follow this pattern. (Edit (image wasn't showing properly): https://ibb.co/8YJ27Jk)
Please see How to add images to a Biostars post to add your images properly. You need the direct link to the image, not the link to the webpage that has the image embedded (which is what you have used here)
EDITED (now that I thought about it more):
It is possible that your gene expression is indeed greatly affected by a homozygous deletion.
If the deleted region acted as a repressor for the current gene, having it missing altogether could explain the raise.
Thanks for the reply! Actually, this gene should've been deleted as well (I deleted an entire structural region via CRISPR and it was confirmed genetically too) . It is making me wonder whether there is off target mapping from STAR?
Visualize the alignments. Look at the region that you supposedly deleted. What do you see there
How exactly was the DEL generated (on molecular biology level)? About what order of magnitude are we talking about (base pairs)? Please give some more details. Are all these data points biological replicates?
Thanks for the reply! Yes, these are biological replicates and the genomic region was deleted or introduced through CRISPR. There are other genes deleted within the region that show the expected trend (no expression for homozygous, decreased for heterozygous, and increased expression of duplication). I just found several anomalies for some reason.