Lab introduction 

Safety

If you are new to the lab there is an onboarding procedure you must complete prior to stepping foot into the lab space. All of our “wet spaces” are biosafety level (BSL2) and we handle the blood and tissues of multiple species including human and non-human primates, zoo animals, agricultural animals and pet species. We also culture microorganisms known to cause illness in humans. As such we maintain BSL2+ safety procedures in these spaces to protect against infectious disease. All prospective lab members must work with their direct supervisor to complete the following:

1) mandated safety training developed by the UIUC Directorate of Research Safety

2) be added to the Brinkworth General folder on Box and review lab SOPs for protocols and materials

3) review the MSDS sheets for the reagents in the lab (General folder)

4) review and sign the lab’s safety plan

5) complete a form accepting or refusing a free Hepatitis B titer and vaccination

Anyone who will be involved in human subject or animal research in the lab will have to complete Institutional Review Board  and Institutional Animal Care and Use Committee trainings specific to UIUC and the projects prior to work. 

We handle dangerous things. Our lab and community are only safe if everyone follows the safety protocols. If you suspect non-adherence, please speak to Jessica.

Communications and Planning

1) be added to the lab email list (email communications. Jessica does this)

2) added to the lab Outlook Planner (experiment schedules, absences, lab management tasks. Jessica or lab tech does this)

3) lab-owned Box folders (Jessica does this)

4) You will be assigned specific times based on tasks in the lab. If you cannot fulfill your task on schedule you must find another lab member to complete that task for you, and communicate with the technician and Brinkworth who will be completing that task for you. Abandonment of tasks is cause for removal of lab membership. 

5) Sometimes student schedules do not map to the experiment schedule. We work with very rare specimens, and run long protocols. Sometimes a sample comes in when it comes in and we process it, regardless of student schedules. As a lab member you are a) expected to try your best to support the lab work as you are able when unexpected changes occur in the schedule – sometimes schedules clash and there is nothing to be done b) if you are a paid member or student trainee you are expected to provide time for the lab during its busiest periods as part of your schedule. 

6) If my office door is open, feel free to stop by to chat etc.. If my office door is closed I am not available at that moment and you should send me an email to schedule a meeting. 

7) When we are running long protocols, I generally make myself available for calls and texts from the team. Certainly call me if there is a critical problem, or emergency. 

Values

 

 1) Hate will not be tolerated. Report any such behaviour/speech/writing/etc. to Brinkworth immediately.  

2) As a group, lab members recognize that we are interdependent. Actions we take and actions we do not have alter our success as a group. If you are a member of this team, you are responsible to all members of the team. 

3) Lab members are committed to helping each other succeed

4) We communicate with one another in a timely fashion. Lab members are expected to acknowledge emails, texts and other forms of communication between other lab members. 

5) We follow through. Lab members complete the tasks they are given, and report back to the team.

6) We recognize that we are the caretakers of people’s tissues and data. We responsible for sharing what we find with our donors, and caring for their materials in a respectful, private and confidential manner. 

7) We recognize that we have a responsibility to any animal we sample to use that sample to the best of our ability. As such, we commit to being prepared to receive it, care for it, complete our tasks around it, maximize the data we can acquire from it, and maintain the resulting data so we can limit the number of animals we access.

8) We work together to maintain a safe and well-functioning lab. That means we clean up after ourselves at the end of experiments and procedures. We do not use someone else’s reagents. We lock doors and are mindful of theft. We schedule equipment. We care for equipment and report damage immediately. We respect and update protocols, safety manuals, articles in progress when asked. 

9) We insist on data transparency and maintenance. Biology is messy. Its data is messy. How we conduct our analysis must be tidy, and easy to understand. It must be complete. 

10) We recognize that our support for trainees is tied to federal funds for specific projects. Trainees are expected to work within funded projects. As a lab we work together to ensure that those projects succeed. 

11) We are responsible to the communities we work with at all stages of a project. Community members are lab members. 

12) We recognize that degrees and degree names are not indicative of lab member value or even knowledge. 

13) We recognize that we should steward the land we complete our work on. Lab members commit to the management of our composting program and pollinator gardens. 

14) Our values and needs will evolve and we will re-examine our thoughts and approach over time. 

Lab Meeting

1) All lab members are expected to attend. While the lab admin will our best to set the meeting a time when all members are available, lab members are expected to hold a specific space for those lab meetings in their schedule. 

General rules and protocols 

Communication methods

1) We use university email for communication. Grad students and safety contacts may communicate with Brinkworth via text as well. 

2) We plan our experimental schedule on Planner. 

3) Specific lab-task training is recorded in the lab safety manual by you and the person that trained you. 

Data storage and back ups

3) All lab documents are stored in lab-owned Box folders.

4) Always store data in its original format (e.g. .czi, .fcs etc.). 

5) No lab data, code, images, tables, text files, or word processing documents are stored on computers in the lab or elsewhere (e.g. laptops, core computers). Documents and images are stored on Box. Sequencing data is stored on the cluster if it is being used and in the archive permanently.  

6) All sequencing data is backed up to external drives as well as the archive when it arrives. Bioarchive folders cannot be renamed. Only Brinkworth manages saving files to Bioarchive 

7) Once a month, live data folders for projects are saved to external hard drives. Hard drives are organized by project. 

Lab manuals

8) Lab notebooks belong to the funder. They must remain intact (no pages torn out), have numbered pages, and be kept to NIH standard (detailed here)

9) When lab manuals are completed, the person who finishes the manual must photograph the manual, convert the images to pdf, compile a pdf of the manual, and upload it to Box under the project under the name, number and inclusive dates of the lab manual. 

10) Per federal rules lab notebooks live in the lab permanently. When you leave the lab, your notebook stays here. 

 

Sample storage and management

11) All tubes to be stored are labeled with the label printer, stored in labeled and bar coded tube boxes. Any tubes stored in racks will be thrown out. 

12) We have a lab labeling standard that must be followed for every sample attained or generated in the lab. 

13)All samples are to be put into the sample manifest with location information upon their generation. 

14) We use a single lab sample manifest. Do not make your own sample manifest for the lab. If you must download the manifest to update it immediately upload it to its position in Box. 

15) Never move the manifest from its location in Box. That causes multiple problems for everyone else in the lab, and collaborators. 

16) Always record what you are doing with samples that are in the manifest as you access them for various protocols (e.g. RNA isolation). 

Purchasing

17) the university rules around purchasing are many. To make the process simpler our lab develops lab orders  in an online spreadsheet available to all lab members. If we need to order something, get a quote and put item and quote number in the order in the sheet. Please let Brinkworth know when the lab orders are ready for submission so she can submit them to the College. 

18) the university asks that we track item receipt. When items are received, the person picking up the package must store the items as per labels and note in the lab order that it was received. 

Protocols

 There are habits you are expected to develop to help you move through these protocols smoothly. You are expected to commit to the following rules and approaches around protocols:

1) read the protocol in advance and review each step of the protocol at each step every time you complete it. Write it the steps out on the hood

2) never ever do any math in your head. Always use a calculator, write things down, use your fingers if you have to. Doing math in your head in the middle of a protocol almost always leads to error. 

3) record any decisions or calculations you make in the lab manual – yes, even if they are little decisions, even if it is the same calculation you have made every week for 13 weeks and you got exactly the same result. Write it down. 

4) never ever copy prior lab manual entries for protocol calculations. Write new entries using new calculations every time. This prevents copying someone else’s error.

5) do not make unilateral decisions about protocol changes (e.g. order of process, cell seeding, wash steps, temperatures…anything). If you think a change will improve the procedures speak to the author and troubleshoot it with Brinkworth. 

6) mistakes happen. Note potential errors in the lab notebook and complete the work. We will assess the possible error at protocol completion. 

7) Brinkworth is always available to help work through a problem. Contact whenever. 

8) Protocols involving live cells can be difficult.  Suggestions and troubleshooting are always welcome, and in some protocols troubleshooting in real time is expected (if you are isolating cells and you do not see cells where they are supposed to be, but rather where they are not supposed to be then you need to troubleshoot in the moment). Hang in there. It gets easier with time. 

 

Data Analysis

1) All analysis is to be recorded and stored in Box under the designated Box folder and saved in that data analysis document in real time. No data outputs or inputs are to be stored on personal computers. 

2) There are a variety of programs available for data analysis recording (Jupyter, R markdown). We store genomic and flow cytometry data analysis in two formats  a) an ongoing R.doc that stores all final code for a process, annotated in plain and complete language as an instructional document b) a pptx file, with the process or resulting image on the slide, and the segment of code that produced it in the notes box. Annotations must list clear descriptive and time stamped data inputs and the location of those inputs and outputs. 

3) All R related inputs outputs must be stored in box file folders with a read.me file that describes to the outsider what is in the folder and what it represents

4) All data output files must have titles that describe the output and the date and time of production in the title. 

5) All visual data analysis (ImageJ/Fiji, differential cell counts) is recorded in spreadsheets. Templates have been set up for this purpose.

6) If the process of analysis is not well annotated and transparent to the team, we will not publish the analysis. 

7) Any data analysis to be shown at lab meetings should be reviewed with Brinkworth first so we can assess it together. 

Education

The lab is research space which is, by definition, a place to learn. The lab is committed to involving and training people at all education levels in our protocols, practices, and findings

1) UIUC undergraduate students can train in various aspects lab research under the credits ANTH444, ANTH445, IB390. Parkland students – I’m not sure what the mechanisms are. Reach out and I’ll look into it. 

2) Starting in 2027 new graduate students are expected to commit to completing their training under an extant funded project. The path looks like this 

 Year 1. Training starts. assigned courses (stats, HPC-short course in transcriptomics (JFB will fund), immunology, evolutionary immunology, genomics), applying for fellowships, learning lab protocols in lab, assemble committee. That summer you will either work with a collected dataset or work in the lab on current data collection

Year 2. Data collection, grant writing, publishing. There will still be courses to take, but you will analyzing data for pilot work and define what the next set of experiments should look like. During period you will also apply for grants. Your grant background will be converted into a review paper. 

Year 3. Data collection, grant writing, paper 2. Review paper would be submitted by now. Odds are there will still be be course credits to complete. With the grant developed and the pilot data analysis completed, you will be complete your preliminary exams. At the end Year three and prior to year four your pilot data should be written into manuscript form

Year 4. Data collection and analysis continues, paper 3. You will apply for the dissertation completion fellowship. During this period you will write the most data filled chapter. This will likely require twice weekly meetings with Brinkworth. 

Year 5. Finish writing and defend. During this period you will finish your most data filled paper and submit it, write an introduction, background and discussion sections of your dissertation. You will defend your dissertation.