Yaamini’s Notebook: Figuring Out ATAC-Seq

Looking at labwork and sequencing options

Previously, I hashed out a plan that involved doing ATAC-Seq with C. gigas tissues. Shelly helped me get some answers on what ATAC-Seq entails from some experts, and put those resources in this issue. The consensus is that:

  • frozen tissue is difficult to work with
  • the protocol will need to be optimized several times for different tissue types
  • it would be easier to optimize a protocol with live tissue

I shadowed Mac today when she worked on her embryo trial! Since there’s a potential that I can do scATAC-Seq, I would need to learn how to dissociate cells. In talking to her, it seems like I’ll need to isolate nuclei no matter what I end up doing, so that’s a better method to look into first. Mac send me a nuclei isolation protocol that I’ll review and figure out how to translate to frozen C. gigas tissues.

Going forward

  1. Determine what kits to use for RNA and DNA extractions and order necessary materials
  2. Test RNA extraction protocol with tissue in histology blocks
  3. Start processing frozen tissues
  4. Extract DNA and RNA from larvae
  5. Identify an ATAC-Seq protocol and start testing it
  6. Figure out what to do with C. virginica sperm and other potential samples

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Laura’s Notebook: Oly methylation analysis, Jan. 29th 2020

From the last meeting with Katherine and Steven, these were my tasks:

  • Re-do MACAU with pre-filtered count files <— DONE
  • Reannontate new MACAU results <— DONE
  • Reannonate DMLs <— DONE (unless I need to re-do DML filter settings)
  • DMG analysis
  • Figure out something comparable to Fst on DMLs and MACAU to do a correlation analysis
  • GO_MWU analysis redo with genes: https://ift.tt/2RDEgvW
  • New methylation distance matrix to include just loci with new 75% threshold
  • Get manhattan distance for just DMLs
  • Get methods down on paper ASAP