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rnabioco / tRNA004

Nanopore direct tRNA sequencing method refinement and RNA modification benchmarking
https://www.biorxiv.org/content/10.1101/2024.07.23.604651v1
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Finalize list of samples to sequence #7

Closed lkwhite closed 10 months ago

lkwhite commented 11 months ago
  1. Jay — tetrahymena
  2. Chloe - Drosophila
  3. Federico - human fibroblast cell line
  4. Jill - E. coli, possibly
  5. Kristin Watt - zebrafish
  6. Laura - budding yeast
  7. Mukherjee lab - human adrenal cell line
  8. Jess Finlay-Schultz - human breast cancer cell line
  9. Elizabeth Spear (maybe) - some kinda microbe?
  10. Shelby can maybe get us T4 infection (Modomics has 8 annotated tRNAs for this)

image

Can we get some S. griseus and/or H. volcanii RNA? Haven't looked yet at which species give us the most novel mods for our buck.

lkwhite commented 11 months ago

I'm also trying to hunt down some L. luteus but it mostly grows in the wild in Portugal. Which does sound like an awesome field trip, but.

lkwhite commented 11 months ago

Honestly this might be faster, I can totally grow & grind up 300 ng worth: https://victoryseeds.com/products/yellow-lupine-i-lupinus-luteus-i

lkwhite commented 10 months ago

Shelby has done T4 and T5 infections for Jill/Kezia to work up. Lupines are growing, may or may not be included in preprint data. We'll call that good enough.