Change this page by clicking the Edit button or refer to the Wiki Support pages for help
For fire or first aid dial "3333"
Security: dial "4444"
Lab plasmids: https://wrightlab.york.ac.uk/home
BSF Wright Lab folder: https://drive.google.com/drive/u/1/folders/1f1J4eR3LjF8PvAFo-aXCoi9ZuKKALBhn
-20 Freezers and Fridges: https://docs.google.com/document/d/1_3aCIoSPGo1BnC542_YAKqA6dTct70fshyltKSLk_d4/edit?usp=sharing
Emergency freezers in L/M1 link corridor (also E021, F019). Emergency fridge in F019.
Freezer alarm contact list and alarm reprorgamming: Steve Howarth
What to do if you are ill and can't come to work: https://www.york.ac.uk/admin/hr/leave-and-absence/sickness-absence/if-you-are-unwell/
Booking annual leave (Flexileave): https://flexileave.app.york.ac.uk/leave/calendar/
Lone worker policy: https://www.york.ac.uk/biology/intranet/health-safety/lone-working/#tab-4
Parcels awaiting collection https://www.york.ac.uk/biology/itsupport/cfm/stores/index.cfm
TC Hood Booking B/L/146A (insect cell culture room). You will need to email Simon Grist to get added to this booking system: https://chembook.york.ac.uk/booked/dashboard.php
Travelling - fill out travel log for insurance: https://www.york.ac.uk/staff/working/insurance/
Useful email addresses
If you would like to send out an email request to the biology department for reagents, plasmids etc, you can use the following email groups:
Last updated: 17/09/2021
|Adam||Enzymes (PCR, RE), pH meter, molecular biology, gel tanks, CL3 protocols and handbook regular revision reminders|
|Cecile||Electronic and physical repository (databases, plasmids), tissue culture room fridge|
|Enrica||Home Office regulated procedures database, microscopes|
|Delphine||Freezers, Lab meeting rota|
|Joe||Plate reader, ensure tissue culture incubator water reservoirs full|
|Cristina||Ordering, cleaning and jobs rota, cell lines, thawing fresh 293 cells, underbench -80 freezer, AKTA Pures|
Cleaning rota for L1 communal lab areas
Gel doc and
|28th January||Team 30|
|25th February||Team 30|
|25th March||Team 30|
|29th April||Team 30|
|27th May||Team 30|
|24th June||Team 30|
|29th July||Team 30|
|26th August||Team 30|
|30th September||Team 30|
|28th October||Team 30|
|25th November||Team 30|
|16th December||Team 30|
Cleaning of these areas will normally be come between 14:00 and 16:00 to avoid disrupting work in these areas.
Lab meeting rota
Last updated: 17/09/2021
|16.12.22||No lab meeting - Parasite@York meeting Jeffares lab|
|06.01.23||No lab meeting - Parasite@York meeting (Kaye lab)|
|13.01.23||11:00||Kelly||Williamson Rooms||Lab meeting|
|20.01.23||11:00||Jo||Williamson Rooms||Lab meeting|
|27.01.23||No lab meeting - Parasite@York meeting (Wright lab)|
|03.02.23||11:00||Remembering Kelly||Williamson Rooms|
|10.02.23||11:00||Delphine||Williamson Rooms||Lab meeting|
|17.02.23||No lab meeting - Parasite@York meeting (Cayla lab)|
|24.02.23||11:00||Adam||Williamson Rooms||Lab meeting|
|03.03.23||11:00||Cecile||Williamson Rooms||Journal Club|
|10.03.23||No lab meeting - Parasite@York meeting (Walrad lab)|
|17.03.23||11:00||Enrica||Williamson Rooms||Journal Club|
|24.03.23||11:00||Cristina||Williamson Rooms||Journal Club|
|31.03.23||No lab meeting - Parasite@York meeting (Crosnier lab)|
|07.04.23||No lab meeting - Good Friday|
|14.04.23||11:00||Vincent||Williamson Rooms||Lab meeting|
|21.04.23||No lab meeting - Parasite@York meeting (Perez Mazliah lab)|
|28.04.23||11:00||Jo||Williamson Rooms||Journal Club|
|05.05.23||11:00||Delphine||Williamson Rooms||Journal Club|
|12.05.23||11:00||No lab meeting - Parasite@York meeting (Fellows)|
|19.05.23||11:00||Adam||Williamson Rooms||Journal Club|
|26.05.23||11:00||Cecile||Williamson Rooms||Lab meeting|
|02.06.23||No lab meeting - Parasite@York meeting (Faria lab)|
|09.06.23||11:00||Enrica||Williamson Rooms||Lab meeting|
|16.06.23||11:00||Cristina||Williamson Rooms||Lab meeting|
|23.06.23||No lab meeting - Parasite@York meeting (Wilkinson and Hewiston lab)|
|30.06.23||11:00||Vincent||Williamson Rooms||Lab meeting|
|07.07.23||11:00||Jo||Williamson Rooms||Lab meeting|
|14.07.23||11:00||Delphine||Williamson Rooms||Lab meeting|
Health and Safety
Last updated: 18/10/2021
York H&S web site: https://www.york.ac.uk/biology/intranet/health-safety/
Safety monitor for L1 is Christoph Baumann
L1 Induction and Rules
Risk assesments and SOP's and general safety
Hard copies of Risk Assessments and training records are kept in the lab and on this wiki
Generic department risk assessment for working with chemicals: https://www.york.ac.uk/biology/intranet/health-safety/chemical-safety-2/risk-assessments-of-chemicals/guidelines-for-risk-assessment/
Overarching "good lab practice" document at York: https://www.york.ac.uk/biology/intranet/health-safety/code-lab-standards/
L1 and BSF labs GM and biological safety RA for working with CL2 kinetoplastids: https://docs.google.com/document/d/1Wbk7vQS8LTrlcu6uwCVYFGOaWaIkdf7I/edit
L1 labs Code of Practice working with trypanosomes (SAPO): https://docs.google.com/document/d/17cQghpJO3PE5tnY1w-h8ZzTYNvAinXh5/edit
CL1 GM work (cloning and protein expression in HEK cells): https://docs.google.com/document/d/1piPtKcdYivYEjDEheX6TnfG2YvyC4Ka6/edit
CL3 work in H block (Code of practice, risk assessment, SOPs): https://drive.google.com/drive/u/1/folders/1XokCpkLSffF6PJbIEzClKrJqU9JL5Cbl
Lab coat and gloves should be worn when undertaking any procedure in the lab.
Safety glasses can be found in the last bay in the top drawer under the plate shaker and should be worn when handling strong acids and bases, fuming and corrosive substances.
A full face shield must be used when handling liquid nitrogen and when taking out heated liquid from the microwave oven. The fume hood is located in the chemical room.
First aid room is in biology atrium near mail room.
Fire sweeper for L1:
Spills, accidents, incidents and near misses
The chemical spill kit and mercury spill kit are located under the main lab sink.
There is a further chemical spill kit and safety signs located near the stores window. Before clearing hazardous spills, check the MSDS for any special measures.
In the event of a mercury spill, evacuate the area for 30 minutes, don protective clothing and respiratory mask before clearing spill.
The mop and bucket are located in the cell culture room.
First aid kits are located in both the office and lab corridors of L1 in the middle of the building.
Accidents/incidents and near misses can be reported https://www.york.ac.uk/admin/hsas/
Accident/Incident and near miss reporting: "It is important that the Campus Health and Safety Service are made aware of any incident on the Campus that has lead to someone being injured or made ill, or to property or equipment being damaged. We also need to know about those incidents that could have led to someone being injured or made ill, or to property or equipment being damaged - a 'near miss'.
Last updated: 01/10/2022
Training records can be found from historical electronic copies of this page
|Technique||Person responsible||Protocol||Risk assesment||Perform||Train others|
|AKTA Pure handling (HisTrap purification, column cleaning/regeneration)||Cristina||AKTA Pure RA||Cecile, Delphine, Cristina, Adam||Cecile, Delphine, Cristina, Adam|
|Avexis screen||Enrica||AVEXIS||AVEXIS RA||Cecile, Enrica, Cristina, Adam||Cecile, Enrica|
|SAVEXIS||Cecile||Cecile, Adam, Kelly, Joe||Cecile|
|Batch his-tag purification||Delphine||Batch his-tag purification||Batch His-tag purification RA||Cecile, Delphine, Cristina, Adam, Joe||Cecile, Delphine, Cristina, Adam|
|BIAcore handling||Cecile, Enrica, Cristina, Adam||Cecile|
|Bioluminescence assay (plate reader)||Delphine||Bioluminescence assay (plate reader)||Bioluminescence assay (plate reader) RA||Delphine||Delphine|
|Blood smears||Delphine||Blood smears||Blood smears RA||Delphine||Delphine|
|Changing gas cylinders||Adam||Gas protocols||Gas RA||Adam||David Nelson|
|DNA gel electrophoresis (agarose/EtBr/SybrSafe)||Joe||DNA Electrophoresis||DNA Electrophoresis RA||Adam, Cecile, Delphine, Enrica, Cristina, Vincent, Kelly, Joe||Adam, Cecile, Delphine, Enrica, Cristina, Vincent, Kelly, Joe|
|DNA/plasmid prep||Joe||Plasmid Preparation||Plasmid Preparation RA||Adam, Cecile, Delphine, Enrica, Cristina, Vincent, Kelly, Joe||Adam, Cecile, Delphine, Enrica, Cristina, Vincent, Kelly, Joe|
|ELISA (BIO-proteins)||Cecile||Adam, Cecile, Delphine, Enrica, Cristina, Kelly, Joe||Cecile, Enrica, Delphine|
|EZ-linked biotinylation||Cecile||EZ-link biotinylation protocol.docx||Adam, Cecile||Cecile|
|Flow cytometry||Adam, Enrica, Vincent||Training provided by TF staff|
|Freezing/thawing cells||Enrica||Protocol||Freezing/Thawing cells_RA||Adam, Cecile, Delphine, Enrica||Cecile, Enrica, Adam|
|HEK293 (E, F, 6E) cell culture (incl. transfection)||Enrica||Adam, Cecile, Delphine, Enrica, Cristina, Vincent, Kelly, Joe||Cecile, Enrica, Kelly|
|Hybridoma generation (fusion, culture, screen)||Cecile||Cecile||Cecile|
|I.P. injection mouse||Delphine||I.P injection||N/A (refer to BSF RA)||Cecile, Delphine, Enrica||-|
|Immunofluorescence||Adam||Protocol||Immunofluorescence RA||Delphine, Enrica, Adam||Enrica|
|In vitro fertilisation (mouse)||Enrica||N/A (refer to BSF RA)||Enrica||Enrica|
|Insect cell culture and transfection||Vincent||Sf21 insect cell culture||Culture and freeze/thawing of cell lines_Protocol_RA||Cristina, Vincent||Cristina, Vincent|
|IVIS||Delphine||IVIS imaging||N/A (refer to BSF RA)||Delphine||Delphine|
|Leishmania culture||Adam||Leishmania RA||Adam||Adam|
|Lentivirus production/ transduction||Adam||Lentivirus RA||Adam||Adam|
|Magnetic beads purification||Adam||Magnetic beads purification RA||Adam, Delphine||Adam|
|Microbiology hood cleaning||Protocol|
|Mouse oocyte harvesting||Enrica||Mouse oocyte harvesting||N/A (refer to BSF RA)||Enrica||-|
|Myeloma/hybridoma cell culture||Cecile||Cecile||Cecile|
|OX68 expression and purification||Gavin||Protocol||OX68 purification RA|
|Parasite isolation from blood||Delphine||Parasite isolation RA||Delphine||Delphine|
|PCR/DNA digest/ligation||Vincent||Adam, Cecile, Enrica, Cristina, Vincent, Kelly||Adam, Cecile, Enrica, Cristina, Vincent, Kelly|
|Percutaneous infection (mouse)||Cecile||Cecile||-|
|Plasmid data upload to lab database||Enrica||N/A||Enrica, Adam, Cecile, Kelly||Enrica, Adam, Cecile|
|Plasmid transformation of competent E. coli||Kelly||Adam, Cecile, Delphine, Enrica, Cristina, Vincent, Kelly, Joe||Adam, Cecile, Delphine, Enrica, Cristina, Vincent, Kelly, Joe|
|Prey normalisation (beta lactamase)||Enrica||Prey normalisation||Prey normalisation_RA||Cecile, Enrica, Cristina||Cecile, Enrica|
|Preparing chemically competent bacteria||Cristina||Preparing competent cells_RA||Cristina||Cristina|
|Protein concentration quantification||Cristina||Protein concentration quantification||Protein concentration quantification_RA||Cecile, Delphine, Enrica, Cristina, Adam, Kelly, Joe||Cecile, Enrica|
|Protein dialysis/concentration||Cecile||Cecile, Delphine, Enrica, Adam||Cecile, Enrica, Adam|
|Protein press||Cecile||Cecile, Cristina||Cecile|
|SDS-PAGE||Vincent||SDS-PAGE protocol||SDS-PAGE RA||Adam, Cecile, Delphine, Enrica, Vincent, Kelly, Joe||Adam, Cecile, Delphine, Enrica, Vincent, Kelly, Joe|
|Coomassie||Vincent||Coomassie staining protocol||Coomassie staining RA||Adam, Cecile, Delphine, Enrica, Vincent, Kelly, Joe||Cecile, Enrica, Adam, Kelly, Joe|
|Subcutaneous injection mouse||Delphine||N/A (refer to BSF RA)||Delphine|
|Size exclusion chromatography||Cristina||Superdex™ 200 Increase 10/300 chromatography||Size exclusion and AKTA Pure RA||Cecile, Cristina, Adam||Cecile, Cristina, Adam|
|Tissue culture||Cristina||Protocol||Adam, Cecile, Delphine, Enrica, Vincent, Joe, Kelly||Adam, Cecile, Delphine, Enrica, Vincent, Kelly, Joe|
|Western blot||Vincent||Western blotting RA||Adam, Cecile, Delphine, Vincent||Cecile, Enrica, Vincent, Adam|
|I.V injection||Delphine||N/A (refer to BSF RA)||Delphine|
Vectors at Geneart and Twist
Last updated: 16/09/2015
To order genes by gene synthesis it is important that the reading frames are preserved. To avoid the need to add flanking bases to your orders this has now been sorted out by defining the correct insertion sites (updated Jan 2023). Please follow these instructions to ordering from Twist: https://docs.google.com/document/d/1sB3sOnEmuHFAhnpXqcPMV_a7o4kVpabDtI90ngrDwOs/edit
|Twist ref:||Geneart ref:||Our ref:||Database ref:|
|N/A||vector1_C819_||Mero-bio (no insert)||V|
|N/A||C820||type II signalpeptide-bio-linker-Cd4||V|
|v1_SP-HLBio-Cd4||p1943_E668||type II signalpeptide-his-linker-bio-Cd4||V75|
|v2_Cd4-BioLH||p0821_D725||rat CD200 - Cd4- bio-linker-his|
|v4_mero-Cd4-COMPBLFH||V087_MTRAP_M770||Mero (MTRAP) - Cd4-COMP-beta-lac-3xFLAG-His*||V87|
|v3_mero-Cd4-BioLH||I078||Mero (RH1) Cd4-bio-Linker-his*||V74|
|_v6_mero-BioLH||P3054_Q942||Mero (RH5-N-term)-bio-Linker-his* (no Cd4)||V|
Network path for Team 30 drive is R:\rsrch\gjw515\lab\T30_Sanger
To map the R drive to a Sanger issued laptop. Sign into EduRoam with your York username and password. Open filed explorer and click map network drive and map the following path. Check the box regarding using an alterate credentials.
Check the box regarding using an alternate credentials.
Log in using "ITSYORK\(Your user name)
Plasmid database templates
Protocol for adding new plasmids to the database: https://docs.google.com/document/d/1RK6L17u5DDLrRoPbrlf_nQbQ0CShldc6/edit
New plasmid upload spreadsheet: https://docs.google.com/spreadsheets/d/1cDr_vuwYYOkmKM2zYUaMcWtN0gG0YmQ1/edit#gid=1830307744
Example template for plasmids P6360 to P6368: https://docs.google.com/spreadsheets/d/1rtuDqQ6CMoorJHB7iRLl7RPru3hcqQfR/edit#gid=133676251
Feature annotation spreadsheet (version 2): https://docs.google.com/spreadsheets/d/171nm31wC6oCVllNdCmYio-hjG92wqI5N/edit#gid=1111209947
Human receptor full-length cDNA collection
The lab has a collection of full length cDNAs corresponding to human cell surface receptors cloned into mammalian expression plasmids.
A publication describing them is here: PMID:31578119. Refer to Supplementary Table 1 for a list of the clones in the collection.
The information to obtain the clones is here: https://docs.google.com/spreadsheets/d/1MJphNoyLrlKSgpJ_Hbfy4TSJ5qkeD54Y/edit#gid=530711501
There 2 full copies (each copy consists of 36x96well plates) of the library as glycerol stocks: a "cherry pick" working stock and a longer term storage "archive" version. These are kept in separate freezers for security. They are stored in the black and orange FluidX plates that can be read by a bar code reader - see bar code on base of the tubes.
The 96-well plate identifiers are the 8 digit numbers beginning with "SA" and then column and row identifiers; these are found in the spreadsheet and printed on the side of the 96-well plate.
There is a working plasmid prep version of the library called "Source plates". These are identified with the plate name e.g. "Tagged 101" or "Untagged 128". These are stored in the -20 freezer with the Wright lab plasmid repository.
Additional information on the plasmids including plasmid maps can be found in the folder: https://drive.google.com/drive/folders/1MnG3OOCXwNC5nF-m6g1TZKwAjust2KWo?usp=share_link
The Wright Lab Facebook group can be found on the following link - please sign up! https://www.facebook.com/groups/357803710988905
Galaxy R incubator, Wolf labs
Current access code for this incubator is 0000.
In case access code is misplaced, to change the access code on this inbubator, follow instructions below:
- Press DIAG then ENG
- Key in 1973 press ENTER
- Tab down to
- USER ACCESS CODE press ENTER
- Then press RESET
- Press EXIT several times to return back to main screen
That will now have removed the pin code from the incubator.
To connect to your TECAN folder:
Important! You will first need to install IT Services' VPN connector called Pulse Secure. Instructions on how to do this are at http://www.york.ac.uk/it-services/connect/vpn/
- Windows 10
- Open File Explorer (press the "Windows" key and E, or type File Explorer in the search box)
- Click "This PC"
- Click "Computer" tab at top and then "Map network drive"
- Select drive letter R
- In folder box enter: \\userfs.york.ac.uk\username
- Do NOT tick the 'Reconnect at Login' box, but DO tick the 'Connect using different credentials' box and then click Finish
- In the "Enter Network Credentials" box, click "More choices", then "Use a different account"
- Enter user name in the form ITSYORK\usernameand then your Uni password. If you are using your own login account on your own PC or laptop, then tick the "Remember my credentials" box. Do NOT tick this box if it is possible for someone else to login to your account on your PC or laptop.
- Click OK.
1. Go to this link and log-in with your standard university account https://uk.ideaelan.com/secure/public/applogin.aspx
2. Press the button to "register" and then follow the prompts for registering. Note that when answering the prompt of what PI/lab you are under, you should search "gjw515" as Gavin's name may not appear.
3. Once you're done registering, use the same link to make bookings for equipment throughout the Technology Facility (https://uk.ideaelan.com/secure/public/applogin.aspx). Under the "Instruments" tab you can tick the boxes next to pieces of equipment you want to view/book, then on the calendar click and drag to reserve a time on that piece of equipment. To finalize your booking you'll need to select a Work Order out of the drop-down list we set up of the lab's standard grants.
4. It's recommended that for your first booking you should email the facility head (for example, Peter O'Toole for cytometry) to schedule a training session. These are mostly for your own benefit, as unlike Sanger there's no further approval forms you need to do post-training.
|Security||01904323333 or 3333 from campus phone|
|Dr Christoph Baumann|
|Dr James Foxemail@example.com||Facilities|
|Dr Marie-Christine Labarthe-Last||CL2/CL3 lab manager|
|David Nelsonfirstname.lastname@example.org||Ext. 8524|
|University H&S services||Ext. 2020|