General Standards & Practices in the lab:

Inventory/storage

• Label everything (solutions, tubes, etc) with contents, date, your initials.
• Absolutely no unlabeled liquids in the lab. This is a safety violation.
• Write the date received on all chemicals and kits as they arrive in the lab. Please be aware that the most expensive supplies (Qiagen kits, sterivex filters, biopsy punches) may be designated by project - let PI know when these arrive.
• Liquids may not be stored above shoulder height. This is a safety violation.
• Label freezer boxes on the front edge, not just the top of the box.
• Label freezer boxes with project and year.

Cleaning

• Bleach + guanidine binding buffers = VERY BAD
• If you made the mess, you are responsible for cleaning it up. This includes washing dishes and putting them away, autoclaving waste, cleaning up old PCR tubes from the freezer, etc.
• Cleaned dishes should be promptly put away once they are dry.
• If you used the last of something, replace it and don’t leave the empty container lying around. ***Also tell PI when something is getting low so I can reorder. Send the catalog number of the item for re-ordering.
• Do not store aquarium supplies at the sink and do not stack the aquarium parts on top of clean molecular biology supplies.
• No gloves in the regular trash.
• Only tips and gloves in the black trash can. No paper trash.
• After sequencing data is received, throw away all cleaned 16S rRNA PCR products. KEEP all original DNA and RNA extractions, cDNA preps, metagenomic/metatranscriptomic libraries.
• Autoclave old cultures and pieces of diseased coral since they are dense growth, but recognize that this isn't required.
• There should be no red bags on the benchtop - we do not have any BS2 level microbes in the lab. You do not need to autoclave the tips from DNA extractions, etc.
• Absolutely no food dishes in the lab area. Use the kitchenette down the hall to clean your dishes. This is a safety violation.
• Do not put any soft trash (kimwipes, paper, etc) in the sharps disposal.
• Do not store anything in the biosafety cabinet. This is a safety violation.

Have a few minutes to spare?

• fill EtOH wash bottles
• wash dishes
• put dishes away
• replace full autoclave waste bags
• autoclave waste
• wipe down apparently dirty/dusty surfaces

Contamination in the lab:

• 70% ethanol kills cells – it does not remove DNA; bleach destroys everything (cells, nucleic acids, proteins)
• RNAses are everywhere – if you are working with RNA, clean gloves and surfaces with RNAse Away and use only RNAse/DNAse-free water and tubes.
• When we are doing projects with illumina sequencing, contamination will easily enter your samples. Dust and spores floating in the air will contaminate media, solutions, tubes, tips, etc. An open container is a contaminated container unless you are using an open flame (which causes the air to flow up and away from your samples) or if you are using a laminar flow or PCR hood (neither of which we have). We can use the biosafety cabinet, but it is designed to keep air from flowing out of it, it is not specifically designed to keep your items contamination free. To use the biosafety cabinet to diminish the chance of contamination, it must first be thoroughly sterilized (spray down with bleach, let it sit a few minutes, then spray down with ethanol to remove the leftover bleach which has the potential to destroy your sample’s DNA). Similarly, wipe down your pipettors, tips boxes, and tube racks with bleach and then ethanol. Do not soak the pipettors in any type of liquid – put the bleach on a paper towel and use that to wipe the pipettor clean. You can then turn on the UV light to sterilize the outside of your supplies. Do not UV enzymes, dNTPs, master mix, or primers as this will damage them. You may UV water. Do not depend on the UV for all sterilization, as it cannot reach all surfaces. Once everything is sterile inside the cabinet, you can use the blower to keep the air inside the cabinet separate from air inside the lab.
• Make sure you process an extraction blank for each project and each Qiagen/Zymo extraction kit. This means you take out an extra tube and process it alongside your samples - it just doesn't get any biomass at the beginning.
• Do not carry extra solutions from one kit to the next. When you open a new kit, use all the new kit components. Label the box and bottles with opened date. The kits should already have a received date too.
• For all work bound for illumina sequencing, use the T3 tubes. Take one 50-pack for your own use and keep it sterile (don’t reach in with gloves, don’t leave it open).
• Gloves are not sterile out of the box. If you are working with sensitive samples – for example, scraping biomass off a coral fragment during which you may have to touch the sample, you should first clean your gloves with bleach and then ethanol (while on your hands).
• Do not reuse gloves and do not leave used gloves laying around on bench tops. Gloves are very cheap - your samples are not.

Lab Notebooks

• All lab notebooks officially belong to the University of Florida. They do not leave the lab when you graduate or move on to another position.
• All lab notebooks should be backed up with digital copies. You are responsible for photographing your lab notebook. There is a lab ipad available for this or use your phone. Deposit lab notebook pages into the lab's one drive. You will be able to take digital copies of your notebooks when you graduate.
• All writing should be legible at all times.
• Always put more information than you think will be necessary in your lab notebook - you never know when minor observations turn out to be very important. Best practices will include writing the lot numbers of the kits used. You don't need to re-write kit instructions, but note the version number of the instructions. For example, all Qiagen kits have dated protocols.

Data storage

Amplicons

• Do not use a capital "R" in sample names submitted for amplicon sequencing. Lowercase "r" is fine. The uppercase R interferes with the loop in the cutadapt script.
• Keep sequencing data files compressed (.fastq.gz) to maximize storage space.
• All raw sequencing reads will be delivered to the PI through hipergator and immediately backed up on dropbox and an external hard drive.
• Raw data is delivered as separate folders for each sample name, containing forward and reverse reads. For your project it is your responsibility to move all reads to one directory. When this has been completed, let me know and I will back up the single directory as well --- these files will be submitted to NCBI before manuscripts are submitted for peer review.

Genomes, Metagenomes, and Metatranscriptomes

• Keep sequencing data files compressed (.fastq.gz) to maximize storage space.
• All raw sequencing reads will be delivered to the PI through hipergator and immediately backed up on dropbox and an external hard drive.
• Raw data files will be submitted to NCBI before manuscripts are submitted for peer review.
• See workflows for QC files that you should keep in perpetuity.

On Hipergator

• Our research computing subscription pays for a limited amount of storage on hipergator.
• Keep sequencing data files compressed (.fastq.gz) to maximize storage space. Most command line programs we use can access the data without expanding the files.
• Backup original files, important intermediate files, and final files on an external hard drive (provided by the lab). Do not keep all intermediate files.

On MEYER_LAB-OneDrive

• This directory is a shared directory from the PI's one drive. Do not remove files from here. Feel free to download copies of what you need.