Journal Club Papers
Lab Rules
General rules:
Be present during normal working hours (9:30 AM-5:30 PM +/- 30 mins) so that your colleagues can find you when they need to. If you need to take time off, please email both Mingxia and Simon ahead of time so that we can plan accordingly.
Back up your raw data routinely. Journals will request raw data (e.g., uncropped western blots with ladders on the side), including your notes, for publication. Flow cytometry will require data for all gating strategies.
Document your experiments carefully, including all details, on a daily basis. Some journals are now requesting this as well.
Use a laptop encrypted by the hospital for confidentiality purposes.
For grant submissions, please send in your draft of the proposal at least four weeks before the deadline. Plan ahead and avoid procrastination. The internal deadline for CCHMC is two weeks before the official deadline.
Check all forwarded emails and sign up for talks/seminars that are relevant to your work.
Reply to emails in a timely manner (usually within a day) and acknowledge receipt of all emails as a courtesy.
For lab orders, if a single item exceeds $500, please ask Simon or Mingxia to confirm before sending the quote to the lab manager.
Ensure a successful presentation at thesis committee meetings, conferences, and division meetings by having your slides ready at least two weeks in advance and scheduling a rehearsal. This will allow sufficient time for feedback and adjustments to enhance the impact of your presentation.
For vacations, please notify the PI at least two weeks in advance for coordination purposes.
Prior to presenting any data at a conference, please check with the PI to ensure alignment with our research goals.
1:1 Meeting Preparation:
Start with the overarching goal of the study and recap of the last meeting.
On each slide, please include: Title- take-home message; Results- your data; Conclusion and potential issues need to be discussed.
Next steps for the following week.
After your 1:1 meeting, please summarize the bullet points during the discussion, and send the next steps ranked by the priority of the work to both Mingxia and Simon by the end of the day.
Lab Meeting Preparation:
Please follow the “Scientific Presentation” format shown below.
Everyone is encouraged to ask questions and give input to make the meeting more interactive.
Journal Club Presentation:
Please include the following FIVE components:
Background: what’s known and what’s not known, what’s the knowledge gap and novelty of the study, what is the research question; Figures: make sure to understand as much details as possible;
Conclusion: summary of the take-home messages;
Pros and Cons: what can we do differently to improve the quality of the article;
Application: What can we learn from this paper to guild our own research projects.
Tissue Culture Maintenance:
Keep Tissue Culture hood and incubator clean. Wipe the surface and glass shield with 70% ethanol and mycoplasma eraser before and after your work.
Always wear a lab coat and gloves while working in the Tissue Culture room.
Refill the consumables and reagents if you use the last bottle/vial and notify the lab manager to order.
Refill the 70% ethanol spray when it’s almost empty.
Clean the waste solution container when it reach ¾ full and add fresh bleach.
No overfilled glass pipette or any sharp items inside the sharp container. When it’s full, replace with a new sharp container and notify the lab manager to call for pick-up service.
Separately dispose the biohazard waste and regular waste into different bins.
Follow the booking schedule on designated Tissue Culture hood.
Turn off the light source for EVOS system and light microscope when you finish using. Or dime the light source for light microscope works as well.
Change back to the bucket rotor for Tissue Culture centrifuge when you finish using the plate rotor.
Lab Archives
This is our digital lab notebook. Please set up an account using your CCHMC credential and share your notebook with me (Mingxia.gu@cchmc.org). Please spend a good effort on maintaining it and keeping it updated. This is important in case there are any audits on our future publications to demonstrate our lab has good record keeping.
Lab Archives also has the most updated protocols (RNA extraction, qPCR, staining, functional assays etc.,) and lab inventory. Please check what we already have purchased in the lab before placing an order.
Lab Orientation
Training (please register and finish within one week):
Research education: https://centerlink.cchmc.org/research/research---tabs/research-education
CITI Training: https://centerlink.cchmc.org/research/research---tabs/research-education/citi-training-information
Biosafety training: http://centerlink.cchmc.org/research/research---tabs/biosafety/biosafety-guidance
Animal training: http://centerlink.cchmc.org/research/research---tabs/veterinary-services
Animal care training: https://centerlink.cchmc.org/research/research---tabs/animal-care-and-use-training
Schedule animal training: https://centerlink.cchmc.org/research/research---tabs/veterinary-services/training
Schedule animal care training: https://centerlink.cchmc.org/research/research---tabs/animal-care-and-use-training/training-requirements---new-research-personnel
Shipping biological materials: https://centerlink.cchmc.org/research/research---tabs/biosafety/shipping-training
ePAS training (this is for submitting protocols/grants): https://cchmc.sharepoint.com/sites/ORCRA/epas/default.aspx
Stratocore account setup (for various core service booking and billings): http://centerlink.cchmc.org/research/research---tabs/stratocore/home and ask help from business office if you have any questions.
Training at the Core Facilities:
*First step: Stratocore set up/login: make sure to have a stratocore account before using any core facility services.
This is the link to all CCHMC core facilities: http://centerlink.cchmc.org/research/research---tabs/shared-facilities-directory
Confocal Imaging Core (CIC): Sarah McLeod, Sarah.McLeod@cchmc.org; Matt Kofron, Matthew.Kofron@cchmc.org
Gene Expression Core (GEC): Steve Potter, Steve.Potter@cchmc.org
Pluripotent Stem Cell Facility (PSCF): Chris Mayhew, Christopher.Mayhew@cchmc.org
Pathology Research Core (PATH): Bonnie Ward, bonnie.ward@cchmc.org
Research Flow Cytometry Core (RFCC): Silva-Lages, Celine (sorting), Celine.Silva-Lages@cchmc.org;
Sarah Croswell (analyzer), sarah.croswell@cchmc.org
Veterinary Services Facility (VET): main office R6182, 513-636-4441, Facility Orientation Request; Wet Lab Training Request.
R 3rd floor shared equipments: Schedule
Business Office (CCHMC Pulmonary Biology)
They will be assisting you with ordering, set up accounts, and grant submission.
Albertz, Unmi (Manager, be NICE to her!!!) Unmi.Albertz@cchmc.org
Maxwell, Patricia (Trisha) patricia.maxwell@cchmc.org
Hankerson, Gabrielle (Gabby) Gabrielle.Hankerson@cchmc.org
Schenk, Kimberly (Kim) Kimberly.Schenk@cchmc.org
Administration (CCHMC Pulmonary Biology and CuSTOM)
They will be helping with any logistic issue, book conference room, and set up meetings.
Pulmonary Biology admin: Erika Smith, Erika.smith@cchmc.org
CuSTOM admin: Olesya Rockel, Olesya.Rockel@cchmc.org
Dos and Don'ts
The path to your paper or grant will be littered with failed experiments. Every failed experiment is a personal opportunity to learn how to mitigate failure. Here are some common mistakes that people have made in the lab, hope we could all learn from them-
Do not leave the medium and reagents in the tissue culture hood and turn on the UV light. The UV could kill the active components in them.
Toolbox
Here are some useful links for single-cell browsers:
Human fetal heart (Day 83): https://singlecell.broadinstitute.org/single_cell/study/SCP1021/single-cell-rna-seq-of-normal-human-fetal-heart#study-visualize
Lung:
LungMAP: https://lungmap.net
Tutorials: https://www.lungmap.net/resources-2/tutorials/
LungMAP Video Tutorials:
https://vimeo.com/641989707/728df71172
https://vimeo.com/697472139/0ede95db2d
Human-postnatal: https://azimuth.hubmapconsortium.org/references/human_lung/
Human/Mouse-various age: https://research.cchmc.org/pbge/lunggens/LGEA_v2_home.html
Mouse (E12-P14): https://lungcells.app.vumc.org/
Human (cell card)-postnatal: https://app.lungmap.net/app/shinycell-lung-cell-cards-human-mnn
Mouse (Stage 21 to adult): https://app.lungmap.net/app/shinycell-mm-timecourse
Endothelial cells:
Lung EC (Human and mouse): http://www.lungendothelialcellatlas.com/
Mouse EC: https://endotheliomics.shinyapps.io/ec_atlas/
Mouse cells:
Other useful tools:
How to write a first-class manuscript
Checking Protocols: protocols.io
Making Animation: Clarafi
Figure Illustration: Biorender
Learn Bioinformatics by Yourself
Bioinformatics for Benched Biologists
Bioinformatics for Benched Biologists II (R edition)
Install R-studio: You can find the package on CCHMC self-service;
Seurat tutorial: https://satijalab.org/seurat/articles/pbmc3k_tutorial.html
AI to debug: ChatGPD: https://openai.com/blog/chatgpt/
Best Practices
During your 1:1 meeting with the PI, please prepare slides that summarize the work you have done over the past week. List the discussion points and future plans. Clarify the action items, and set clear expectation on both sides.
If you are not certain about something, always ask your colleagues or the PI first. It is easier for us to solve small problems together before they become big problems.
Be responsive to your emails. Some emails are time-sensitive, try your best to respond within a day.
Be proactive and plan things ahead. Make sure you have enough cells/reagent to carry out the experiment before you start.
Do not try to get everything done by yourself. Collaborate with others who have the expertise and learn from them.
If someone helped you out, make sure to give them credit in your presentation and publication.
Find the project you are truly passionate about and WORK HARD. Doing research in NOT a 9-5 job.
Scientific Presentation
Following this format during your 1:1 meetings with the PI as well as the lab meeting presentations will help you think clearly , read effectively, catch pitfalls in study design and get good feedback from the group.
1. Title Slide: The general subject of your research project.
2. Background and rationale: What is known, what is unknown, and why is it important to answer the unknown questions (2-3 slides in bullet form with crisp points or illustrations).
3. What is your overall mechanistic hypothesis followed by specific mechanistic hypotheses you have investigated to date and a summary of the results of your completed to date (1-3 slides).
4a. Current Hypothesis under investigation since last lab meeting, including background and rationale if necessary (2 slides).
4b. Experimental Design (1-2 slides including additional background slide if necessary to explain a technique). 4c. Preliminary or Final Results to date related to current hypothesis (Clear data slides ± statistical evaluation if appropriate) (Give number of animals, cells, passage number conditions).
4d. Interpretation of results obtained and future studies if necessary, specifically related to this hypothesis.
5a-d. Current Second Hypothesis under investigation since last lab meeting. 5 a-d addressing issues described in 4 a-d.
6. Current Third hypothesis under investigation (6a-d, etc).
7. Future hypotheses and how they will be tested to complete your project, e.g., investigations of novel findings in human tissues, animal models, etc., (1-2 slides)
8. Acknowledgement Slide
Master Your Oral Presentation by Avoiding These Top 10 Traps
TRAP #1: Knowing no one. If it's a national meeting of some kind, introducing yourself to every attendee as they come in may not be possible. However, you could meet some of the attendees (20-50 people) as they come in the room prior to the start time. Doing that will provide them an opportunity to learn something about you, as well as show them that you value them as a person in the audience.
TRAP #2: No illustrations. Some presenters today use no illustrations, and this is not a good strategy. Illustrations are fine to use if used in appropriate places. Perhaps high points in your talk. If you have three major points you're trying to make, you should illustrate those three major points. For real life experiences, you could use history, movies, books you've read, parables that everyone has heard as little children, pictures, videos, whatever it might be, as those are good sources of illustrations too.
TRAP #3: Going overtime. There's no excuse for running over time. If a question and answer runs over time, one technique might be to say: "I know you're busy, but for those of you who can stick around, I can answer additional questions. If you can't stay, no problem. I'll try to reflect what questions were asked and provide my answers by email later," or something to that effect.
TRAP #4: A lifeless presentation. Breathe fire into your presentation. Make your presentation like a movie if you have to. Think about the illustration that captured people's attention, then think about where can you can build a climax into your presentation and how you can effectively present that. There is a whole wealth of information out there to help you. It's also very easy to take pictures and videos in your lab if allowed. You can reflect some animation in your talk by adding pictures and videos.
TRAP #5: Not speaking from the heart. Reading the slide doesn't very well communicate to the important degree that you need to if you're up there talking. So reading from the slide is not a good way of communicating at all. The audience will feel more confident about your knowledge level if you can talk about a subject without having to look at every point or bullet on the power point.
TRAP #6: Jumping off the main topic. Deviating from the main presentation points gets all presenters from time to time, especially if someone asks a question. If a question is asked during your presentation which is not related directly to the point you are trying to make, you might just have to say "I will gladly answer that question for you at the break, or at the end of the presentation. Come see me then." It's not a very fulfilling thing for that particular audience member but it might be what you have to do in order to move on in a timely way with the material that you're presenting.
TRAP #7: Being dull. Enthusiasm can save the day if in fact you have a very dull topic. Are you enthusiastic about what you're talking about? Are you just standing there presenting data. Is it
dull data? Liven it up a little bit. You might add humor to achieve that, but your tone will also help to infuse enthusiasm to your talk. You might consider abandoning the podium and using a remote microphone. This is very common nowadays, but movement on the stage will also add life to your presentation.
TRAP #8: Not using humor. Humor is difficult for many presenters to incorporate because in science, you don't necessarily think the content is funny. It's just data right? Well it doesn't have to be funny but you could add some humor. Humor is sometimes easy to gauge from the audience itself. Look for humor in the situation if needed. Remember, your effectiveness will increase as you engage with the audience. If you're truly comfortable in your skin, humor will probably come quite naturally.
TRAP #9: No eye contact. You should get as much eye contact in, remember the acronym, SOFTEN. Soften your audience so that they'll want to have eye contact and you'll want to have eye contact with them. Here's a refresh on what SOFTEN stands for: S is for smiling. An O is for open, rather than closed posture. The F means lean forward. The T in SOFTEN
is touch (shaking hands for example). Then, of course, the E is for eye contact. Finally N is
for nod. You can say "okay" from time to time by the use of just a nod towards the audience.
TRAP #10: Winging it. Prepare well. Remember what Ben Franklin said: "By failing to prepare, you're preparing to fail." No presenter wants to be a failure in what they're presenting. This is often overlooked, but preparation is key. You may have groundbreaking data, but if you're not prepared to present it in the best way possible, the consequences can be disastrous. Sometimes, you may only get one chance, so take the time to prepare well.
