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
Now you want to know if the primer sets can be used for other species. To do so, we can extract the target template sequence from the pig transcriptome data and compare it for those of other species.
#2 The effect of genetic variant ## Ensembl Mission: You found a genetic variant in your sequenced individual. You want to investigate the potential effect of the variants.
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):
[1] Rcpp_1.0.8.2 bslib_0.3.1 compiler_4.1.2 pillar_1.7.0
[5] later_1.3.0 git2r_0.29.0 jquerylib_0.1.4 tools_4.1.2
[9] getPass_0.2-2 digest_0.6.29 jsonlite_1.8.0 evaluate_0.15
[13] tibble_3.1.6 lifecycle_1.0.1 pkgconfig_2.0.3 rlang_1.0.2
[17] cli_3.2.0 rstudioapi_0.13 yaml_2.3.5 xfun_0.30
[21] fastmap_1.1.0 httr_1.4.2 stringr_1.4.0 knitr_1.37
[25] sass_0.4.0 fs_1.5.2 vctrs_0.3.8 rprojroot_2.0.2
[29] glue_1.6.2 R6_2.5.1 processx_3.5.2 fansi_1.0.2
[33] rmarkdown_2.13 callr_3.7.0 magrittr_2.0.2 whisker_0.4
[37] ps_1.6.0 promises_1.2.0.1 htmltools_0.5.2 ellipsis_0.3.2
[41] httpuv_1.6.5 utf8_1.2.2 stringi_1.7.6 crayon_1.5.0