A long time ago, at a conference far far away... I had a conversation with a student who lamented that research seems full of gatekeeping and that it is hard to replicate studies and methods, or even fully understand them, because the details in manuscripts are often too few. I generally agree. When I started a post-doc and later a faculty position, I wrote our lab manuals (our 'standard operating procedures') and field templates either from scratch or by modifying documents that were given to me by mentors. Here, I'm sharing some of the lab protocols and templates we use in the lab and field. I hope that someone finds them useful and can use these as a starting place. These are in Word or Excel format. Download them and modify them as you see fit.
Links below:
Foram cleaning protocols for single shell laser ablation icp-ms analysis
Bug juice recipe (for processing sediment trap samples - at least that's what we use it for)
Plankton tow processing instructions
Water sampling instructions for stable oxygen and carbon isotopes and trace elements
And various spreadsheets/templates
We also have instructions for processing MicroCT data using Fiji (aka imageJ) on our outreach website
Cleaning Foraminifera for Laser Ablation:How to clean a foram... let me count thy ways. There is a LOT of literature available for how best to clean foraminifera for various applications and analyses. The literature is fairly thorough, but it's kind of nice to have some protocols in a single place. We wrote a 'cheat sheet' for general instructions we use for prepping forams for laser analysis.
Bug juice recipe: This recipe is for an oxidative cleaning step that makes it easier to get the forams out of sed trap sticky goo. This step is performed after the sed trap samples are split and the split is being processed (picked) for calcifiers. The bug juice doesn't completely get rid of all of the organics (some people ash their samples, we don't), but it makes it easier to pick the forams/pteropods if your sample has a lot of organics (marine snow, fecal pellets, etc). The samples should be picked of all swimmers (copepods, larvae, etc) before the bug juice step.
Plankton tow processing: There are many ways to process plankton tow samples, and they depend on what you plan on doing with the samples, what you want to analyze, etc. Plankton tow samples can be immediately picked on board, fixed with buffered formalin, picked then frozen, fixed in ethanol, etc. Choose your fixative wisely - for example, if you want to know if your forams were alive at the time of collection, use formalin because ethanol will bleach them and it's hard to tell the alive vs. dead specimens. If you want to analyze boron, don't buffer with sodium borate. Included here are two sets of instructions:
Plankton Tow Log - a basic spreadsheet for info we collect when we do plankton tows
Depth calculator for estimating the amount of line out if you're doing an oblique tow - uses the angle of the line
Foram culture logs for spinoseand non-spinose species. This includes details for what we track during daily observations (cyto color, spines length, symbionts, chamber status (full, new, etc.)