Last updated: 2022-04-25
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Mission: You want to investigate if TP53 gene is expressed in a particular tissue of pig and want to design a primer set for its cDNA.
Go to:NCBI and search for “Sus scrofa TP53”.
Now you can see the gene information, exon-intron structure and gene/progein IDs.
Also when you scroll it down, you can see the expression pattern of this gene in varios tissues.
RPKM is a unit for gene expression
Furthere below, you can see relevant publications and expected function of this gene.
Now let’s design a primer set to amplify the cDNA. Put the mouse cursor on the gene image, and copy and note the mRNA ID (NM_21824.3)
And go to:NCBI primer blast
https://www.ensembl.org/Salmo_salar/Info/Index
VEP.
Variants.
Assume that you found a variant in your sequenced sample
Graphically Friendly to Non-model species.
sessionInfo()R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] workflowr_1.7.0
loaded via a namespace (and not attached):
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[29] glue_1.6.2 R6_2.5.1 processx_3.5.2 fansi_1.0.2
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