Kartzinel:Policies

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Lab Safety Training & Requirements

Please check with Tyler as you develop your research plan. Given the diversity of research interests in our lab, each researcher may have to meet different responsibilities. Fulfilling some of these responsibilities may require several weeks of planning before lab work can begin.

University Training & Requirements

To work in the molecular lab, minimal requirements at Brown include:

Brown University Undergraduates

If you are an undergraduate with interest in joining the lab for an independent study, senior thesis, or other opportunity, this section includes some brief tips and links for you. Undergraduates will have the opportunity to develop independent project ideas and/or contribute to ongoing projects where opportunities allow. We love to collaborate with students from many concentrations, and can facilitate research involving fieldwork, lab work, and computational research; but not all such opportunities are available all the time. Students joining the lab will be expected to:

  • Check out the information on independent studies, honors theses, and other research opportunities by reviewing the Biology Undergraduate Education and IBES Undergraduate Education pages.
  • Contact Tyler early in the process to identify research and training opportunities in the lab.
  • Participate in our weekly lab meetings, even before research begins. This will give you insights into what the lab does, what opportunities may be available, and what research strategies are likely to succeed. The more time you spend with the lab, the more opportunities you will have.
  • Develop a research proposal together with Tyler, which can be used to obtain research funding for internships, independent study credit, and thesis research. This is especially important if you are interested in field- or lab-based research. At Brown, relevant funding opportunities include the Voss Undergraduate Fellowship from IBES, Royce, UTRA, LINK (including international internships with our partners). If funding for independent research is not available, there may be occasional opportunities to participate in ongoing research led by postdocs and graduate students. Please ask.
  • If planning to work in the molecular lab: complete the Lab Techniques Basic Skills Workshop and at Brown (relevant previous research experience may be demonstrated instead).

Equipment Use Policies

Ground Rules

  • Only use equipment that you have been trained to use. If new to the lab, or if running a new type of experiment, please check with senior members of the lab (i.e., Tyler, postdocs) before you begin. This will help ensure consistency within the lab.
  • If you are using lab equipment and it breaks, or if you notice something not working properly, report it right away. Tyler can always offer feedback on the best course of action.

Scheduling Equipment

  • Major work stations can be reserved a day in advance. This includes, but is not limited to, the biosafety cabinet, the PCR cabinet, the thermocycler, and the gel station.
  • All equipment use should be scheduled on LabAgenda, and this is the only official way to reserve equipment; please do not assume you will have access to equipment unless you sign up in advance. This calendar is organized and maintained by the current 'Molecular Lab Leader'; please contact this person for access.
  • For same-day use, equipment becomes 'first come, first served'. A person can announce their plans on the white board, or post a sticky, or get to work.
  • Electronic field equipment can be reserved. For extended use, for example on an international field trip, please ensure the equipment is reserved at least 2 weeks in advance.
  • The golden rule always applies -- be kind and supportive to your teammates -- you should use the equipment when you sign up, avoid monopolizing the equipment to the exclusion of others, and consider yielding your reservation if another user has an urgent need.

Concluding the Workday

  • Ensure all equipment you used is CLEAN. You may need to read sections on the biosafety cabinet, PCR cabinet, gel rig, and other equipment for specific details.
  • Ensure all equipment you used is OFF. This includes major pieces of equipment like the biosafety cabinet, and also minor pieces of equipment like the vortex. Centrifuges and power packs should be powered down using the button on the front and then switched off using the toggle switch in the back.
  • The lights in the main lab are on a motion sensor and so you don't need to turn them off when leaving (in fact, you can't). However, the lights in the freezer room and post-PCR room are on a switch -- please do remember to turn them off whenever you leave.

Lab Contacts (Summer/Fall 2018)

  • Brian Gill: Ordering supplies, obtaining stock aliquots.
  • Bianca Brown: Molecular Lab Leader.
  • Patrick Freeman: Lab group organizer.
  • Code and Data Working Group: Patrick Freeman (chair)

Lab organizational resources

  • Quartzy: Submitting pre-approved orders for purchase, lab-wide sample inventory.
  • LabArchives: Your digital lab notebook for strategies, recipes, images, results.
  • LabAgenda: Scheduling use of equipment in the molecular lab.
  • IBES lab server: Where raw data in active use should be backed up and shared.
  • [I will add links to the list when it is complete]

Sample Labeling Policies

Sample inventory numbers

All samples entering the lab require a sample inventory number. This number will be used to track the samples physical location in the lab as well as any data that we generate from the sample. Again, this policy applies to ALL samples that come through the lab. This includes samples collected by (and even belonging to) our collaborators.

The requirement of keeping lab-wide inventory numbers does NOT mean that we will replace or overwrite any pre-existing sample identifications. Indeed, it would be a mistake to overwrite anything that is on a tube already -- especially tubes that come from our collaborators. It is possible for a sample to have an inventory number in addition to other forms of identification (physical names, sample IDs from collaborators, etc.)

Please note that it is possible to pre-label and pre-fill sample collection tubes or plates based on assigned inventory numbers (e.g., we do this routinely with zymo tubes).

To procure new inventory numbers:

  • Log into our lab's Quartzy inventory (https://app.quartzy.com/login). If you need access, ask.
  • Click “Inventory” and then filter to only show samples.
  • You will see items with inventory numbers in the form of TK#######, where "#" corresponds to a sequential set of numbers that include leading zeros. (We have a long way to go before we run out of numbers with leading zeros, but can convert to an alphanumeric system when needed.) Determine the next available inventory number: the lowest number that has not been used.
  • Create entries in Quartzy for the numbers that you will use for your samples so that no one else inadvertently uses the same set.
  • Typically, you will know exactly how many numbers you need and you should only reserve this many (e.g., 50 for a batch of zymo tubes; the count of samples provided by a collaborator). Please try to avoid "guessing" if reserving sample inventory numbers in advance of collection.
  • To create an entry in Quartzy, follow the instructions for downloading a template excel file and then uploading your additions.
  • Check that your Quartzy entries were created properly, and ask for help if you are unsure.

To edit existing inventory numbers:

  • When editing metadata pertaining to a sample in Quartzy, pay special attention to the difference between the "item name" column (i.e., the sample ID in our lab) and the "serial number" column (i.e., the number linked to each unique Quartzy entry).
  • You must edit information about existing inventory numbers directly in the template -- do not upload new information about an existing sample using a different inventory number.

Please note that we are only using Quartzy for lab-wide inventories. That is, only to keep track of existing inventory numbers and their physical locations. Each project must develop a data management plan in consultation with Tyler -- all additional metadata and results must be archived according to this plan.

Printing labels

  • We have a lab printer dedicated to labeling large numbers of sample tubes (N >50). Henry Johnson can provide you the necessary drivers to print from you computer.
  • Unused TK numbers are stored in the box next to the printer. Each lab member has an envelope to store their respective TK numbers. Please store your claimed TK numbers (duplicates and others) in your respective envelopes. All claimed TK number stickers not in an envelope with be disposed.

Types of sample containers

  • Freezer boxes: ...
  • 96-well plates: ... Place labeled plate inside freezer box or ziplock bag -- and label those as well -- to keep the exterior of your plates clean.
  • Collection tubes (zymo tubes, cryo tubes, falcon tubes): ... If appropriate, these should be pre-labeled and pre-filled before collections begin (see policy on sample inventory).
  • Sample tubes (snap-cap tubes): ...

Ordering Supplies

Policy: Orders for general lab supplies will be made through our lab's Quartzy account. The lab member responsible for coordinating orders this year is Brian. Brian places standard orders on Monday, so please make sure all orders are approved and submitted by Friday morning.

Ordering process: First confirm with the PI that your standard order is approved (kits, reagents, field supplies). Then submit the request via Quartzy. Urgent and unusual orders require approval from the PI and will be submitted directly.

Delivery: All lab members are expected to check for deliveries in the IBES main office on a daily basis to help ensure packages arrive in the lab without delay. The person responsible for placing the orders will mark them as received in Quartzy and is responsible for making sure they are unpacked and put away. Cooperation is key to ensuring sensitive orders are handled appropriately (e.g., enzymes that must be kept in the -20).

Project Planning

It can be useful at the project-planning stage to have a general sense of the options, costs, and time investments associated with common workflows in the lab. Here are a few benchmarks:

Metabarcoding

Short amplicons: this includes one of our most common markers, trnL-P6, which has an insert size range of about 10-140 bp (median/mode = ~51-52 bp). Assume a project size of one plate (96 reactions), including all positive controls, negative controls, and blank extracts. Prices are approximate and account for both our current discounts and anticipated price hikes. We often have to factor in additional costs for setup, troubleshooting, and quality assurance (e.g., blank extracts, re-runs, etc.).

  • Lab-based costs:
Step Cost Supplier and part Time
Extraction $5.50 per sample Zymo Soil/Fecal with Expedition buffer (suppliers) plus consumables half-day (up to 30 samples; 24 is comfortable and totals 96 extracts after 4 rounds)
PCR $1.10 per sample polymerase (supplier), dNTPs (supplier), primers (supplier) half-day (up to 96 at a time)
Electrophoresis $10 per gel (can run up to 96 samples/gel) agarose (supplier), buffer (supplier), ladder (supplier), dye (supplier) half-day (up to 96 at a time)
Total $643.60


  • URI-based costs (approx. internal pricing):
Step Cost Supplier and part
Shipping $100 per library
Two-step PCR and checks $1420 per library
Library cleanup and validation $200
Paired-end Illumina MiSeq run using the 300-cycle kit $1400 per library
Total $3120


Waste and Container Disposal

Many sections of this wiki include specific details about how to dispose wastes and containers. Here are some general guidelines:

  • Bottle containers with caps (e.g., ethanol, bleach, buffer, water) can be reused for disposal of liquid biological waste. When the bottle is empty, rinse thoroughly and place near the liquid waste satellite stations in the pre- or post-PCR spaces. Do not recycle. Do not leave on the bench.
  • Tips and tubes. Each lab user needs to carefully dispose of consumables in a manner that is pre-determined to be appropriate for the project. If a lab user encounters consumables left over from someone else's project -- on the bench, on the floor, near the trash -- please dispose of these items as if they are biological waste. Report to the PI and mention it to other recent lab users to hold us all accountable.

Shipping and Receiving

Receiving packages

It is the responsibility of the person expecting a package to pick it up and store it properly. If the package comes when the receiver expects to be away, it is that person's responsibility to coordinate with someone else in the lab and ensure there is clear communication about how to unpack/store the contents. Whenever new packages are received, they should be removed from the shipping box/envelope and stored in the incoming area so their respective owners can claim when ready.

  • Incoming package area in the lab main lab: bench to the left when you enter the lab from the office.
  • For temperature-sensitive reagents: -20 top shelf.


Dry Ice

Shipping DNA on dry ice may be necessary in some cases. Confer with Tyler for new types of shipments. This type of shipping requires pre-planning. Here is an overview of the steps involved.

  • Dry ice shipments require an Environmental Health Safety (EHS) representative for packaging (lab members that do this very often may be trained as "authorized shippers").
  • EHS appreciates an email 72 hours in advance to schedule packaging. Send this email to all three of the following individuals: Shannon Benjamin shannon_benjamin@brown.edu, Linda Olmsted linda_olmsted@brown.edu, Linda Laporte linda_laporte@brown.edu.
  • Complete the EHS shipping form, a dry ice safety sheet, and a waybill from the shipper (FedEx, UPS, USPS; please compare prices). Please note that the EHS representative that packages the shipment must be listed as sender on the waybill.
  • Dry ice can be obtained from BioMed stock room. They do not store large quantities of dry ice, so ensure that dry will available on the day of your shipment.
  • Dry ice must be in a Styrofoam box, placed within a cardboard box. There should be little to no space between the styrofoam and cardboard boxes. Containers can be reused as long as they are in good condition and previous markings are covered.
  • Prior to EHS arriving: weigh and record the weight of the box and dry ice separately (in kg); ensure all forms are complete; obtain clear packing tape but do not close the box prior to approval from EHS.

International Fieldwork