Last updated: 2022-04-25

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0 Introduction

1 Primer Design

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.

NCBI

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.

https://www.ensembl.org/Oryctolagus_cuniculus/Gene/Variation_Gene/Table?db=core;g=ENSOCUG00000015307;r=12:106859193-107318499;t=ENSOCUT00000015301

Assume that you found a variant in your sequenced sample

https://www.ensembl.org/Oryctolagus_cuniculus/Gene/Phenotype?db=core;g=ENSOCUG00000015307;r=12:106859193-107318499;t=ENSOCUT00000015301

Graphically Friendly to Non-model species.

UCSC - check tandem repeats, liftOver (convert genetic regions between species between genome versions), in-silico PCR, etc. Variants.

https://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=hub_51387_GCA_905237065.2&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=HG993260.1%3A143240818%2D143254033&hgsid=286603936_wMmBef9vkWmZKbnIKQ8k97LFAdv3

https://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=galGal6&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr5%3A22418650%2D22435035&hgsid=286782955_c9foS2olaWM8jALUbsP1WlLZC7Dt


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     

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8.2     rstudioapi_0.13  whisker_0.4      knitr_1.37      
 [5] magrittr_2.0.2   workflowr_1.7.0  R6_2.5.1         rlang_1.0.2     
 [9] fastmap_1.1.0    fansi_1.0.2      stringr_1.4.0    tools_4.1.2     
[13] xfun_0.30        utf8_1.2.2       cli_3.2.0        git2r_0.29.0    
[17] jquerylib_0.1.4  htmltools_0.5.2  ellipsis_0.3.2   rprojroot_2.0.2 
[21] yaml_2.3.5       digest_0.6.29    tibble_3.1.6     lifecycle_1.0.1 
[25] crayon_1.5.0     later_1.3.0      sass_0.4.0       vctrs_0.3.8     
[29] promises_1.2.0.1 fs_1.5.2         glue_1.6.2       evaluate_0.15   
[33] rmarkdown_2.13   stringi_1.7.6    bslib_0.3.1      compiler_4.1.2  
[37] pillar_1.7.0     jsonlite_1.8.0   httpuv_1.6.5     pkgconfig_2.0.3