This website is a work in progress - we aim to provide access to all standard protocols and procedures used at the Goodman Lab. We are part of the Department of Public & Ecosystem Health in the College of Veterinary Medicine at Cornell University. Our lab is located at the Baker Institute for Animal Health. If you’re a member of the Goodman Lab, then you can collaboratively edit any of these protocols. This wiki-style approach gives us a central place to develop our lab protocols, while always keeping the most up-to-date protocol in one convenient and publicly accessible place.
If you’re not part of the lab, no worries, you can still peruse the site to see our protocols. Comments and feedback are welcomed! Please reach out to us at [email protected].
*Template inspired by the Beiting Lab at PennVet Center: https://protocols.hostmicrobe.org/. Please check out their course on RNAseq: https://diytranscriptomics.com/
**Disclaimer (written by Tina herself): the majority of the organization and R tutorials on this page is written by Tina Yu, a Cornell 2023 graduate who spent 4 years in Laura’s lab, working as an undergraduate student first, then as a full-time research assistant. If you know Tina in real life, you would not be surprised by how lengthy some of the explanations are, because as introverted as Tina is, she talks and digresses too much. But she also believes that scientific communication requires thorough explanation since she was once a student who knew nothing. Please bear with her, and she promises she won’t take any feedback personally :)
Illumina Library Prep checklists
Nanopore for bacteria (and fungi?) - work in progress
bs_cli_v1.6.0 download biosample -i 710163032 -o . --extension=fastq.gzgalaxy-upload --history-name FungalGenomeAssembly S2v3B_S30_L001_R*_001.fastq.gzfirst, login:
/programs/czid/czid login
Metagenomics pipeline
/programs/czid/czid metagenomics upload-samples -p "mastitis-ENV" \\
--sequencing-platform Illumina --metadata-csv metadata.csv -m 'Metadata Name=Metadata Value' ./
metagenomics tells czid which pipeline to runupload-samples allows you to upload a bunch of samples at once-p tells czid which project you want to upload to--sequencing-platform signifies what was used to sequence the samples—metadata-csv contains info for each sample name you have - these files are required by czid, and make sure the value is in the dictionary set by czid (https://czid.org/metadata/dictionary)-m flag is not necessary./ signifies the directory where the data liveAMR pipeline
/programs/czid/czid amr upload-samples -p "mastitis-ENV" --metadata-csv metadata.csv ./