|
WELCOME TO THE QI LAB (8/2/2007- present) You have reached the Qi laboratory (pronounced as "Chi"). We are located at the 4th floor of Biotechnology Building, but we will move to the 3rd floor in the near future (our home department is in Savage Hall). Please click here to check out who else is on the 4th floor and where common equipments are located. Hopefully, you will find the website informative and helpful. Please contact Ling if you have any comments and suggestions. For new lab members, please take time to read through this guide.
Computers CO2 Databases DNA oligos DNA sequencing Dry ice
Ice Keys Liquid nitrogen Literature Mann library Microscopes Mission statement Mouse training Mouse purchasing
Office supplies Purchasing PCR/Q-PCR
Radiation training Radiation safety Remote access Seminars Shipping Shared equipment Trash/medical waste Antibodies Cell Lines
Undergraduate students
- : Our laboratory aims to explore the physiological role of stress response and immune response in the context of obesity and diabetes using genetic tools, to produce new insights into the etiology of these diseases, and to bring a standard excellence to all that we do as an individual scientist and as a laboratory. We strive to create an environment that is fair, respectful, courtesy, collegial and conducive to learning and testing new ideas.
- The first step of this program is to fill out the registration form and then return to Diann LaPoint (dfl4; 3-3529) for Module I training and any specific mouse training as applicable per Diann. Assuming if they are on your approved protocol, they must have already filled out their Risk Assessment Form (pdf) and sent to EH&S. They will need to do Module II training (Orientation) which can be set up with Sylvia Allen (sa63; 4-4399). Once through all training, you will be given access to our mouse room - give Sylvia the ID numbers. Please also remind Ling that he needs to add you to the lab mouse protocol. Of note, there are many useful information on the CARE website: http://www.research.cornell.edu/care/sops.html#anesthesia
- If you have never been on a permit before at Cornell, the first step is to take the required Rad Safety class. It's offered once per month and the schedule and sign up is on Safetybase. The class is over 2 days so be sure to sign up for both Day 1 and Day 2, 3hr each. There is a quiz after Day 2 that you take online via Blackboard. Then you can complete the New User Form (.doc) and the safety checklist on the back. Hand it to Cindy, who will take care of the rest.
- If you just want to have access to the e-journals, then set up Cornell VPN is sufficient. The client program and the setup details for either PC or Mac can be found here: http://www.cit.cornell.edu/services/vpn/. If you want to set up remote access to our lab server, please follow this instruction [VPN instruction for Mac.doc] for Mac and this instruction [VPN instruction for PC.doc] for PC. But be sure to disconnect it when you are done with it before you put the computer to sleep. You can access to the lab databases from anywhere in the world including home by log onto the Biotech server using VPN, but you can't surf anywhere while you are on it. Disconnect when you are done.
- We have several lab databases for cell lines, plasmids, primers, antibodies, mouse tissues, viruses, purchases, and chemicals at https://mbgdna2.calsnet.cornell.edu/fmi/iwp/res/iwp_home.html. Please refer to those databases when you are looking for something - try to save your time (there is a "search or find" function in every database). Everybody will be responsible for the updates of the Cell line, Plasmid and Tissue Databases when a cell line or construct is made and deposited to the lab cell line or plasmid bank; Cindy for the rest of Databases. Cindy will maintain all lab DNA and antibody stocks. When the DNA is low, please inform Cindy. This is crucial for the organization of the lab and for us to become as efficient as we possibly can, so please try your best to help us maintain them.
- Click here for reading list; please send the pdf to Ling if you come across a great paper.
- Cornell has a wonderful library service and has all the books you ever need. Go to the URL http://www.mannlib.cornell.edu/. click on "library catalog". You can also request them buy or subscribe new books and journals by contacting Reference Desk. They also offer classes for photoshop or statistics, which you may find useful as well. Please try to use this wonderful resource, you will enjoy it.
- For equipment in the common area, sign the log sheet for everything you use if there is a log sheet. Clean up after yourself. If you are using other lab’s equipment, always first check with other labs and make sure you know how to operate. Try not to break it. If you do, no big deal, try to fix it first. If not fixable, bring the issue up to Ling. He will approach the lab PI and get it fixed asap, so it won’t affect other people’s experiment. One thing I find important to remember is that this is a lab, a team; and we need everybody to be considerate of others. Just remember that and you will do just fine.
- Gel-doc: use the one in Rm 419 - next to John Lis's lab.
- Electroporator: use the one in Rm 417B - John Lis's lab.
- Dark room: for gel slice - in Rm 469 next to the seminar room; for film processing - use Rm 330 (right off the stairs on the right-hand side).
- High-speed centrifuges: use the one in common equipment rooms (Rms. 428 and 456) on the 4th floor.
- Centrifuge for 500ml bottle: Use our adaptor and special conical bottle to spin down adenoviral infected cells in common equipment Rm. 428.
- Bacterial shakers: use the one in common equipment Rm. 428 for miniprep and maxiprep cultures.
- Cold room: there are two next to our lab. We mainly use the one on the left-side of the lab for storage of bacterial plates, culture media and sonication (Rm. 452); and the other one (Rm. 443) on the right-side for IP and western blot shaker.
- Everybody is expected to attend weekly lab meeting. This semester lab meeting are held on Tuesday at 1:30pm in Rm 180. Everybody can present either a published paper (journal club) or their data (lab meeting). There are other seminars around the campus which lab members are encouraged to attend: Metabolic group seminar (the 3rd Tuesday 2pm every month), Molecular Nutrition seminar (every Wednesday at 4pm in Savage 200) and VERG seminars in Vet school (once a month on Tuesday noon). There are also Monday 12:20pm, Wednesday 12:30pm and Friday 4pm seminars in the Biotech Building.
- Regular lab members (graduate students, postdocs and technician) will be provided with a MacBook laptop; however, the lab will not be responsible for any upgrades (flat-screen cinema display, memory, Hard drive, etc). Undergraduate students and rotation students will bring their own computers. For any request related to new lab member setup, computers, printers and server, please ask Cindy to send request online at http://www.cals.cornell.edu/cals/cals-it/remedy.cfm. Choose "Molecular Biology and Genetics" department. Please do not call or email them directly.
- Send out via Fedex by filling out the form (get the account number from Ling, if we have to pay for it). Drop off the package outside of the Steve Sparling's office. Use UPS ground if it is not perishable nor urgent. UPS store is in the Cornell Bookstore.
- All lab-related purchasing needs to go through Hui/Cindy, including the Biorad (Biotech), Invitrogen (Biotech) and Qiagen (Vet school) stockrooms. For common lab reagents/supplies, write on the dry erase board under the "ORDER" section. For some specific reagents, write on the binder on Cindy's desk with detailed purchase info, and she will place the order after consulting with Hui. When purchasing radioactivity, be sure to write on the order with “Radioactivity” and Cindy will email the order to Bev. If it is urgent, be sure to communicate that to Cindy and then to Bev. We also have blank POs for VWR and FISHER - Cindy can directly call custom service to place the order.
- Ordering is done online now if it is from standard vendors. No details yet. Talk to Ling if you need to order mice.
- KEYS to the lab/building and after-hour access: You need to get keys to the building and the lab (445). Fill out the form [pdf], ask Cindy to sign it and contact Steve Sparling (ss110) for keys, $5/key and up to $10. Lab will not pay for it, which gives you a motivation to return the keys after leaving the lab. You will also need to have access to the building afterhours and weekends - for that, just email Steve Sparling (ss110) with your school ID number and he will set it up for you.
- You can get most of lab supplies from Savage Hall. Here is the list of things DNS supplies. Write on the dry erase board what you need and then Cindy will contact either Bev (bgg3) or Evi (ems93).
- ICE: It is next to the bathrooms on each floor. There are two of them on each floor.
- DRY ICE: It is on the 2nd floor of the Biotech. You have to weigh and log it. It will be charged to the lab account.
- We get it from our LN tank (the one we store cell lines) and Steve Sparling will fill the tank every week. For cell storage, we have two 35L tanks, stored under the benches.
- We get CO2 tanks from Airgas. Once it is low, notify Cindy who will email them at cornell@airgas.com (account #, P card#, location and quantities). They will be delivered the next day. Two tanks are ordered each time. One tank can last over 4-5 months at the current user rate.
- we purchased a tissue culture inverted Zeiss AxioObserver fluorescent (green- GFP/FITC only) microscope, which has fluorescent and phase contrast capability for tissue culture plates and slides. It is a very delicate equipment, please do the following: There are core facilities for confocal and fluorescent microscopes. Other labs may have microscopes that we can use.
- You can order the primers any time you want from Operon - download the order form (oligo order form.xls). After filling it out as shown, please send it to Yin by 2:00pm. She will combine all orders from the lab at the end of the day (before 3:00pm). Right now, we use Operon because they offer free overnight shipping with $.18/base. The turnaround time is about 2-3 days.
- DNA needs to be pre-mixed with primers: place 1µg of plasmid DNA and 8 pmole of primers (=1.6µl of 5µM working stock) in a screw cap vial, bring the volume up to 18µl with H2O. Note: based on my experience, measuring miniprep DNA concentration is not necessary - just add 8.4µl miniprep DNA + 1.6µl 5µM primer + 8µl H2O, without measuring DNA concentration. Do not use TE. We have several standard primers (T7 promoter, T3, SP6, M13F and M13R) and primers to sequence the cloning products for pGL3-Basic, pGEX-5X, pSuper, pSuper-U6 and PXP2 on the sequencing primer rack at -20C freezer - the stock is 100µM. Get an account with BRC by registering at (https://cores.lifesciences.cornell.edu/user/login.php). Charge to lab account (ask Cindy for the number). Once you fill out the work request form, an order number will be given/sent to you. Put the numbers on the bag and then drop it off at the sequencing core facility on the 1st floor (the room right below us). They charge $4/sample. If you don't mix DNA with primers, they charge $5/sample. The quality of sequencing data is not that great - about 700bp; so if you have over 1.5kb cloning product, consider using another internal primer to sequence. If a reading fails, call them asking for a rerun.
- For any cloning, please first try pfu polymerase (Stratagene) and add 5% DMSO to your reaction (please check "lab protocols" under lab server). Pfu is the most reliably polymerase I have used so far; don't use any one from Invitrogen. For regular PCR (genotyping and testing primers), please use the Taq we got from Dr. Long's lab. For 10µl reaction, use 0.1µl Taq (100X) + 1µl PCR buffer + 0.2µl 10mM dNTP + 0.2µl 10µM primer + 4µl cDNA or 1µl gDNA. FOR RT-PCR, we are adapting to Jeff Pleiss' lab reverse transcriptase and their system. For For 96- and 384-well assays, we will use Pleiss lab system. Ask Yin/Hui for help on this. Right now, we have Biorad demo MyCylcer 96-well unit - so use it. In the future, we will use the one in Rm. 469. For 384-well plate, please use the BRC core facility on the 1st floor (the same room as DNA sequencing). Go sign up the time slot one or two days before your experiment. If you don't use that time slot, please cross it out right way. They charge $25/plate.
- please refer to the handbook for details. Just remember: to keep good log on what you use and how much you use; make sure no contamination occur; if contamination does occur, clean it up; if major spill occurs, contact Ling and Radiation Safty Officer. For emergency, call 911 - directly dial 911 on any phone. Cindy is responsible for the monthly wipe-test and book-keeping, and she is also the person who is in charge of training.
- (1) Bacterial plates need to be collected in a waster bag and autoclaved and then put in the black waste trash can outside of the elevator. (2) pipet tips need to be put in a box container and taped it up and label it with "plastic tips" and "Qi Lab" - leave it outside of the elevator. (3) pipets (5, 10 and 25ml) need to be put in a box container and then put in a red hazard bag and leave it in the autoclave room with a tag on it. (4) medical waste from the TC room: put in red hazardous bag. For more information about medical wastes, please download this guide [doc]. (5) the box container: please break it down and leave it in the dumpster outside of the elevator. For other regular trash, please remember “recycle, recycle, and recycle”.
- Undergraduate students: We will limit 2 undergrad students for research at any certain time. Application for research opportunity should be sent to Ling via the "Contact us" page. This should include a paragraph describing your future goal, the reason to choose this lab, the biology courses taken and your cumulative GPA.
- Antibodies: Antibodies are stored in either 4C or -20C (check the database for the exact location). Aliquots are made for some antibodies. We normally use the antibody (in 5% milk/TBST) for 2~3 times. Please save the antibody and put the date of use on the original tubes so we know how many time it has been used. If the antibody has been there for one month, then toss it and make a new one. Please organize your antibody tubes every month or every two weeks.
- Cell Lines: For mammalian cell line, please ask Cindy for a vial of cell line. Freeze down couple vials for yourself. For bacterial competent cells, Haibo made SUPERcompetent cells a while ago, so please use 20µl only for your regular ligation/ transformation - 50µl aliquots.
My job is to provide a best working environment for everybody to enjoy in the lab. Please feel free to let me know if you have any concerns, questions or suggestions. Have a great semester, Ling The Qi lab 9/7/2008 |
