Matt:LabNotes/2013-11-27

From ZhangLabWiki
Jump to navigation Jump to search

RT RAB7A Primers[edit]

  • RT ACTB experiment (Matt:LabNotes/2013-11-14) was inconclusive possibly due to cell fixation
  • ACTB target (on primary rolony) dye probe stock is almost gone so going to try same experiment with RAB7A
    • Considered using EGFR and other cancer genes but those padlock probe targets are thousands of kbp away from TSS which further complicates the purpose of this experiment

Primer Design[edit]

  • Choose primers that are 10bp long while minimizing GC content and ~200bp, ~300bp, ~500bp, and ~1000bp
  • RAB7A mRNA target sequence: CAGAACTTGGACCTTCTCGCTTCTGTCCTCCGTTTAGTCTCCTC
    • This is base 125-177

mRNA RAB7A 220b: CGCGTTTGAA
mRNA RAB7A 300b: ACTCATGAAC
mRNA RAB7A 510b: CAACACATTC
mRNA RAB7A 1000b: TTACACCCCA

RT primers[edit]

RT_RAB7A_220b: TTCAAACGCG
RT_RAB7A_300b: GTTCATGAGT
RT_RAB7A_510b: GAATGTGTTG
RT_RAB7A_1000b: TGGGGTGTAA