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Buckley lab protocols for conducting SIP studies

License: MIT License

Shell 3.19% HTML 89.40% CSS 7.42%

buckley_lab_sip_project_protocols's Introduction

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.

Updating non-markdown versions of protocol files

Please don't edit the Word or html files directly!
The markdown files (*.md) serve as the template files for all of the other formats (eg., html or docx).
The bash scripts (eg., md2html.sh) will convert all files ending in '.md' to a specified format.
- Example usage: ./md2html.sh
  - This will creat a html file for each corresponding markdown file.

Working in the lab

Pipeline steps

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
If DNA: CsCl fractionation
- CsCl_fractionation
Else if RNA: CsTFA fractionation
- RNA_SIP
Nucleotide quantification:
- Picogreen
Nucleotide sample concentration
- speed-vac
Pippin Prep
- Pippin_prep
Fraction nucleotide quantification:
- picogreen
MiSeq library prep:
- Illumina_barcoding_protocol

Others

Cellulose farming
- Cellulose production
  - CelluloseProductionProtocol
- Cellulose grinding:
  - CelluloseGrindingProtocol
Plant stimulant
- Substrate_Additions_MicrobSuccession
Soil geochemistry

Workflows

Bulk DNA sequencing of the 16S rRNA gene

Microcosm -> gradient fractionation -> 16S rRNA gene sequencing

Nucleotide extraction
Optional: Concentrating via speed-vac
PippinPrep
Nucleotide quantification via Picogreen
CsCl_fractionation
- Including desalting
Nucleotide quantification of fractions via Picogreen
16S rRNA amplicon library prep
- For automated generation of the Excel files needed for the PCR assay, see the fractionSelectFor16S-PCR.ipynb notebook in the SIPdb repo.

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