Buckley Lab SIP protocols

Printing protocols (conversion of protocols to PDF)

• View any Markdown file on GitHub, then in your URL bar of your browser replace the github.com part of the URL with gitprint.com
• The Markdown file will be rendered as a PDF for easy printing or downloading.

Working in the lab

• General expectations of lab etiquette
  • lab_etiquette
• General expectations of undergrads working in the lab
  • undergrad_expectations
• General lab tasks commonly completed by undergrads in the lab
  • general_lab_tasks
  • Lab inventory checklist
    • Use the Inventory.xlsx file located at ./working_in_the_lab/Inventory.xlsx

HR-SIP pipeline general workflow

• Soil sampling

  • soil_sampling_protocol

• Microcosm setup

  • Ashley's priming experiment setup (Fall 2013)
    • SIP_microcosm
  • Nick's full C-cycle pilot experiment setup (Fall 2014)
    • SIP_fullCyc_pilot_microcosm
  • Nick's 2nd full C-cycle experiment setup (Fall 2015)
    • SIP_fullCyc2_microcosm

• Microcosm headspace CO₂ measurements (via GC-MS)

  • CO2_batch_run

• Nucleotide extraction

  • DNA_RNA_extraction_Protocol

• Nucleotide quantification

  • Picogreen

• [Optional] Nucleotide concentration

  • speed-vac

• Pippin Prep

  • Pippin_prep

• Nucleotide quantification

  • Picogreen

• If DNA: CsCl fractionation

  • CsCl_fractionation

• Else if RNA: CsTFA fractionation

  • RNA_SIP

• Nucleotide quantification

  • Picogreen

• MiSeq library prep

  • Illumina_barcoding_protocol
  • For automated generation of the Excel files needed for the PCR assay, see the fractionSelectFor16S-PCR.ipynb notebook in the SIPdb repo.

Unfractionated sample 16S rRNA amplicon sequencing workflow

• Nucleotide extraction

  • DNA_RNA_extraction_Protocol

• [Optional] Nucleotide clean-up

  • Sephadex column clean-up

• Nucleotide quantification

  • Picogreen

• MiSeq library prep

  • Illumina_barcoding_protocol

Other protocols

• Cellulose farming

  • Cellulose production
    • CelluloseProductionProtocol
  • Cellulose grinding:
    • CelluloseGrindingProtocol

• Plant stimulant

  • Substrate_Additions_MicrobSuccession

• Soil geochemistry

  • pH
  • organic_content
  • water_holding_capacity