Question: How to Find Fungi Housekeeping Genes?
gravatar for johdgy
11 days ago by
johdgy0 wrote:

Where Can I Find A Large Amount Of Fungi Housekeeping Genes? I want to find an internal control gene for Cryptococcus RT-qPCR.

rna-seq sequence gene genome • 106 views
ADD COMMENTlink modified 11 days ago by Joe15k • written 11 days ago by johdgy0

Please be more specific. What data do you have, which conditions, do you have bioinformatic skills? in any case, what did you try, any literature search yet? Checked conserved genes that are frequently used in mammalian samples?

ADD REPLYlink written 11 days ago by ATpoint26k

I have seen from the literature that seven housekeeping genes of Cryptococcus are selected for MLST typing. I am not sure whether these seven housekeeping genes are suitable for internal reference genes of RT-PCR.

ADD REPLYlink written 11 days ago by johdgy0

thanks for your quick reply. I am new in bioinformatics.

ADD REPLYlink written 11 days ago by johdgy0

No problem, we all were beginners at some point. Still, what data do you have? Do you have any NGS data? If not I suggest you browse the literature and get in contact with a bioinformatician to download published RNA-seq data from your species and try to identify genes that have high expression between several conditions but no evidence for differential expression. These could then serve as internal controls.

ADD REPLYlink modified 11 days ago • written 11 days ago by ATpoint26k

Thanks for giving me the path´╝îI should download the RNA-seq date first. Maybe it's not easy to solve for me

ADD REPLYlink written 10 days ago by johdgy0
gravatar for Joe
11 days ago by
United Kingdom
Joe15k wrote:

I think the simple answer here is refer to the literature. Generally you need to look at conserved genes Involved in central metabolic or reproductive pathways such as DNA replication.

This cannot be learned from bioinformatics alone.

ADD COMMENTlink written 11 days ago by Joe15k
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