Submitting 10 casein and FAM20C in pD1214 plasmids for sequencing 30Sep2014

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September 30, 2014: DNA pick-up by Sequetech to sequence 16 samples, detailed below

  • Location: BioCurious
  • Participants: Rachel (set up sample pick-up), Emi (gave samples to Sequetech rep)
  • Aims: Confirm correct DNA sequence of our casein and FAM20C inserts in pD1214 vector. Trouble shoot Electra cloning negative control positive colonies (See Cloning bovine beta casein, Fam20C (Kex + & -), from 27Sep2014, "Results and Discussion" September 28, 2014.) Confirm identity of unclearly labeled DNA, prob. hKcasein Kex+ in pD1214.
  • Sequencing Strategy & Methods:
    • Submitting 10uL aliquots of 16 samples, detailed in table below, including 10 new casein and FAM20C in pD1214 constructs.
    • Sequetech rep. collected samples at ~2:00pm today.
    • All except hkk+R to be sequenced in two reactions: the forward (with primer TEF-264-FW) and reverse (with primer PMYR3) directions. Sample hkk+R sampled in single direction as was likely the sample already sequenced in both directions, September 5, 2014.
      • TEF-264-FW is a custom primer synthesized through Sequetech: primer sequence recommended by DNA 2.0, suppliers of pD1214. This primer will be maintained in-house for future sequencing reactions. (Note change from sequencing described August 6, 2014, as previous forward primer, Alpha-factor 146-forward, anneals to the FAKS sequence, now inside our redesigned DNA inserts.) See for primer map.
      • PMYR3 is an in-house Sequetech primer.
Primer Sequences 
 Binds to TEF promoter and reads through in the 5'-3' direction (N-terminus of signal peptide).
 Binds to the terminator (CYC1) and reads through in the 3'-5' direction (C-terminus of casein).

Location of sequencing primers indicated by small purple arrows on map of pD1214: PD1214 Map.png

Details for 31 sequencing reactions on 16 samples:

Samples details from Sequetech sequence pick-up, 30Sep2014.png

Sequencing Analysis Summary Table (October 1, 2014)

Screen Shot 2014-10-01 at 4.42.46 PM.png

Clone 9A is also poor. Need to remove from stocks.

  • Discussion: Of the 11 sequencing reactions we were able to evaluate (excluding all FAM20C, as insufficient length, and Electra cloning negative, as didn't align), there were confirmed issues with 3/11 (27.3%): incorrect sequences for bovine alpha S2 Kex+ (#3) & human beta (#4.2) and what looks like poor template DNA for human kappa Kex- (#5). Given that rate, suggest prepping and submitting two separate clones for each construct in the future.