Lab Handbook

Welcome to the Lan Lab. We study how RNA-dependent processes maintain genome integrity and how their disruption creates vulnerabilities in cancer. Our research brings together RNA biology, R-loops, DNA repair, genome stability, and cancer immunity, with the goal of translating each discovery into a biomarker, therapeutic target, or treatment strategy.

This handbook explains how our lab works day to day so that every new member knows what to expect and how to get started. It is a living document that will evolve with the lab. If anything is unclear, incomplete, or outdated, please let us know so we can improve it.

Two expectations stand above all others: conduct careful, honest science, and treat every person in the lab with respect. Everything else in this handbook follows from these two principles.

We value thoughtful, productive work rather than long hours for their own sake. Research does not always fit neatly into a fixed schedule, and experiments will often determine the rhythm of your week. Plan your time responsibly around your experiments, cells, animal work, shared instruments, and commitments to others.

• Regular lab hours are 9:00 a.m.–5:00 p.m. We expect lab members to be generally available during these hours, while recognizing that experimental schedules may sometimes require flexibility.
• Keep the lab informed of your schedule. If your schedule differs from regular hours or changes significantly, make sure the people you work with know when you will be available.
• Take time off. Rest and time away from the lab are important. Please discuss planned holidays with Dr. Lan in advance—ideally 1–3 months ahead for longer trips—and arrange appropriate coverage for ongoing experiments, cell lines, or animal cohorts.
• If you are sick, stay home and recover. Let Dr. Lan and anyone directly affected by your absence know as early as you reasonably can. We do not want anyone coming to the lab sick.

Weekly Lab Meeting

Everyone from the lab will present their work in progress. The meeting is held every Wednesday starting at 3 pm.

Journal Club Meeting

A lab member will present a paper and everyone will pre-read the paper and discuss together. The journal club is held biweekly on Friday 12:30pm.

Joint Lab Meeting

Members from different groups present and discuss unpublished work. Each meeting will feature one assigned lab member from one of the participating labs, who will give a 45-minute presentation followed by discussion. The joint lab meeting is held biweekly on Tuesday at 9:30am.

A result that cannot be reproduced is not a reliable result. Your research records belong to the lab and must remain complete, organized, and understandable after you leave.

• Record every experiment in your lab notebook on the day it is performed. Include the research question, protocol, reagent lot numbers, instrument settings, raw output, observations, and conclusions.
• Store all raw data in the designated lab storage system. Never keep the only copy on a personal laptop or instrument computer.
• Use clear and consistent file names so that any lab member can easily identify and locate the data. Include the date, project, sample, and replicate number.
• Keep analysis code with the corresponding data, and document the software and version used for the analysis.
• Back up your data before traveling and before performing any major reanalysis.

No experiment is worth risking an injury. Duke requires appropriate safety training before you work with certain materials, and our lab requires all necessary training to be completed before you work independently.

• Complete all Duke safety training required for your work before conducting your first experiment. Links to the required training will be provided when you join the lab.
• On your first day, familiarize yourself with the locations and proper use of the eyewash station, safety shower, spill kit, and fire extinguisher.
• Report all incidents and near misses to the lab manager on the same day, regardless of how minor they may seem. We encourage prompt and honest reporting and do not penalize anyone for reporting a safety concern.

The lab depends on shared equipment, reagents, and resources. Treat them responsibly and leave everything in good condition for the next person.

• Reserve shared instruments before use, and promptly release your reservation if your plans change.
• Log your use whenever an instrument log is available, and clean the instrument and surrounding workspace after each use.
• Label every reagent you prepare or open with the date and your initials. Properly dispose of expired or unusable materials.
• If you use the last of a reagent or supply, notify the lab manager promptly so that it can be reordered.
• Register every plasmid, cell line, and mouse line in the lab registry, including the appropriate plasmid map, genotype, and other relevant information. A stock that only one person can locate is effectively lost.
• Always ask permission before taking or borrowing reagents or materials from another lab. Document any applicable Material Transfer Agreement (MTA).

Authorship should reflect meaningful contributions to the work. Expectations about authorship should be discussed early and revisited as the project develops, rather than being left until manuscript submission.

• Authorship is based on meaningful contributions to the study design, data generation or analysis, and/or interpretation of the results, as well as participation in drafting or critically revising the manuscript and approval of the final version for submission.
• Individuals who make valuable but more limited contributions that do not meet the criteria for authorship should be recognized in the acknowledgments, with their permission.
• The first author is generally the person who has made the largest overall contribution to the project and takes primary responsibility for preparing the first draft of the manuscript. Dr. Lan will determine the final author order after discussing contributions with everyone involved and will communicate the rationale clearly.
• Discuss authorship expectations at the beginning of a project and revisit them as the work progresses, particularly when the main figures and conclusions begin to take shape. If questions or disagreements arise, raise them early so they can be addressed openly and fairly. Authorship concerns are much more difficult to resolve at the time of submission.

Everyone eventually moves on from the lab, and a thoughtful handover protects your work, supports your colleagues, and helps ensure that your projects can continue successfully.

• Give Dr. Lan as much advance notice as possible so that there is sufficient time to plan for a smooth transition and handover.
• Prepare a written summary of each project before you leave. Clearly describe what has been completed, what remains in progress, the next recommended steps, and where the associated data, analysis code, and other materials are stored.
• Leave all original lab notebooks, raw data, plasmids, cell lines, mouse strains, and other research materials with the lab. Make sure everything is clearly labeled, organized, and registered in the appropriate lab records. You may keep copies of your own data when appropriate.
• Before your last day, discuss any unpublished work with Dr. Lan and agree on who will complete the remaining experiments, prepare the manuscript, and take responsibility for submission.
• Clean and organize your bench, work area, shared storage spaces, and freezer boxes. Clearly label any materials that will remain in the lab and dispose of materials that are no longer needed.
• Keep in touch after you leave. Former lab members remain an important part of our lab community, and we are happy to recognize you as a lab alumnus and follow your future accomplishments.

Expectations run both ways. You can expect mentorship, support, recognition, and a safe working environment.

• One-on-one meetings. Regular meetings to discuss your research, progress, and career goals.
• Timely feedback. Clear feedback within a reasonable and communicated timeframe.
• Constructive guidance. Honest, specific, and respectful feedback focused on the work and next steps.
• Career support. Guidance on projects and career development, timely reference letters, professional introductions, and interview or presentation practice.
• Recognition and credit. Appropriate credit for your contributions in publications and presentations.
• A safe lab. The training, time, and equipment needed to work safely.

Most problems are easier to solve when they are raised early. Open and respectful communication is encouraged.

• Day-to-day communication.
• Scientific questions. Start with your lab colleagues or bring the question to lab meeting. Discuss project-specific questions with Dr. Lan.
• Lab concerns. Bring concerns to Dr. Lan or the lab manager whenever possible. If the concern involves Dr. Lan, or you prefer to speak with someone outside the lab, Duke provides independent resources.

Using these resources will never be held against you:

• Office of the Ombuds - Confidential, informal, and neutral support.
• Office for Institutional Equity (OIE) - Resources for harassment, discrimination, and sex-based misconduct, including Title IX matters.
• Department of Molecular Genetics and Microbiology - Department-specific guidance for reporting concerns.
• The Graduate School and Office of Postdoctoral Services - Guidance for students and postdocs on academic, training, and appointment matters.

• Set up your Duke ID, building and lab access, and keys. [Dr. Lan: who arranges access]
• Activate your Duke NetID and email, and gain access to the lab’s shared drive and calendar.
• Schedule required safety training and complete a lab safety walk-through.
• Set up your assigned bench, desk, and freezer space.
• Meet with Dr. Lan to discuss your starting project and initial goals.
• Meet the lab members and learn who manages each shared instrument.
• Read this handbook and ask about anything that is unclear.

• Complete all required training for your work.
• Perform the core protocols for your project under the guidance of an experienced lab member.
• Set up your lab notebook and data folders according to lab standards.
• Present a brief project plan at a lab meeting.
• Prepare the first draft of your Individual Development Plan (IDP).
• Meet with Dr. Lan to review your first month, discuss progress, and set next steps.
• Complete any required lab-specific certifications.

Your project is the work. Your career is the point. The lab supports your development beyond your current research.

• Individual Development Plan (IDP). Complete an IDP during your first month and review it annually with Dr. Lan. Define your career goals, the skills you need, and your plan for developing them.
• Fellowships. Applying for fellowships is an important part of your training. Discuss opportunities and timelines with Dr. Lan early, including F31, F32, and K99/R00 awards when appropriate.
• Conferences. Aim to present your work at least once a year when possible. Practice your talk or poster at a lab meeting beforehand.
• Teaching and mentoring. Mentoring junior researchers is valuable professional training. Discuss the commitment with Dr. Lan to ensure it remains balanced with your own research.
• Reference letters. Request letters at least 3 months in advance and provide your CV, the position or opportunity description, and the deadline.

Good science requires a healthy and supportive working environment. We aim for sustainable excellence, not short-term productivity at the cost of well-being.

• Work-life balance. Rest matters. Respect evenings, weekends, holidays, and colleagues’ time outside the lab.
• Inclusion. We welcome people of all backgrounds, nationalities, genders, and beliefs. Different perspectives strengthen our science.
• Accommodations. Discuss any accommodations you need with Dr. Lan, including those related to disability, caregiving, religious observance, or visa requirements.
• Communication. English is a second language for many of us. Be patient, ask for clarification when needed, and communicate respectfully.
• Respect. Harassment, discrimination, and bullying are not tolerated in this lab.
• Well-being. Duke provides confidential support through the Personal Assistance Service (PAS) and Counseling and Psychological Services (CAPS). Seeking support is encouraged when you need it.
• Lab community. We occasionally organize lab lunches, dinners, and holiday gatherings, such as Thanksgiving and Christmas celebrations, to spend time together outside of our daily research.

Acknowlegements

This handbook follows the structure of publicly shared lab handbooks (Aly Lab, Peixoto Lab, Maestre Lab) released under Creative Commons licences. The text is the Lan Lab's own.