User:David Johnston Monje/Notebook/Maize Endophyte Biofertilizers/2011/11/15

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Remains of the Day

  • Localize all tomato soil DNA and use ITS1F and ITS4 primers on them. Also use the phyla specific primers with ITS5-FAM. Save for cutting with HhaI but also order both MaeII and BfaI (and/or BstNI) or HaeIII or DdeI, which together used in a double ITS fragement digest cover the diversity very well.
    • OK, so I found a bunch of DNA (but not all?): There's a box of 35 tubes called "Tomato Vine Decline DNA" with tubes labelled as random numbers in the 7000s or TVD field X. This is likely contemporary with 48 other samples numbered 7000 - 9000 (Tilbury amendmant tomato samples apparently). There's another box filled with 24 tubes labelled TVD X. And then there's another box with 45 samples labelled in the 8000s representing rhizosphere soil from the grafting trial, plus 12 soil samples representing soil from strawberry fields "Santa Maria".
  • Set up and perform some sort of protocol development trial for EtOH vs kit with more reps (or review current data to see if it can support the idea already).
  • Simple explanations are the best - so gDNA contamination is the cause of the false positives - need 30 min incubation with gDNA wipeout to eliminate that from RNA before making cDNA. See photo