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Emergency

For fire or first aid dial "3333"

Security: dial "4444"


Contents




Lab Databases


                                 


           

Cell Bank: https://docs.google.com/spreadsheets/d/1Igchpea8v5S2M1nYv5ErEHiPOABPPS0-univA7_LPqM/edit#gid=1622568477

HO numbers: https://docs.google.com/spreadsheets/d/1kGjXN7PcBrYTNk72L3D_6ZaLeHU60WFlkZoIq_mLB4g/edit#gid=521310156

Lab plasmids: https://wrightlab.york.ac.uk/home

Reagent database: https://docs.google.com/spreadsheets/d/1fYByAPJZXL3jRaUHM0nswj-1mJr4VbHctIUpFLV5AKo/edit#gid=0

BSF Wright Lab folder: https://drive.google.com/drive/u/1/folders/1f1J4eR3LjF8PvAFo-aXCoi9ZuKKALBhn

Freezer contents

-80 Freezer: https://docs.google.com/spreadsheets/d/1zMMZzrPBOaX_aWLqODd0Idgi9Hm6Hx7vSf8Gt-3vDdU/edit#gid=0

-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

Stores order form https://docs.google.com/forms/d/e/1FAIpQLSewp7Wam6ZZ-I4miwCh4czVVUN3we4VSwF_FSGlRXsHnrgEsw/viewform

Stores catalogue https://docs.google.com/spreadsheets/d/1TRsZD0g_d823hR22DFz0vv2NFSoOzDMeDISq6pQlMBw/edit#gid=0

TC Hood Booking https://calendar.google.com/calendar/u/0?cid=eW9yay5hYy51a19lMGgxMGY5MzQydXNhdDgyNHQxZ2p2bG5xMEBncm91cC5jYWxlbmRhci5nb29nbGUuY29t

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:

biol-res-associates-group@york.ac.uk

biol-res-students-group@york.ac.uk

biol-technicians-group@york.ac.uk

Lab responsibilities

Last updated: 17/09/2021

Adam Enzymes (PCR, RE), pH meter, molecular biology, gel tanks, CL3 protocols and handbook regular revision reminders
CecileElectronic and physical repository (databases, plasmids), tissue culture room fridge
EnricaHome Office regulated procedures database, microscopes
DelphineFreezers, Lab meeting rota
JoePlate reader, ensure tissue culture incubator water reservoirs full
CristinaOrdering, cleaning and jobs rota, cell lines, thawing fresh 293 cells, underbench -80 freezer, AKTA Pures

Vincent

Protein press


Cleaning rota for L1 communal lab areas

Last updated:  

Date

Fridays

for 2022

Chemical and

Sonicator room

Cold room


30 degree 

room

37 degree

room

Gel doc and

centrifuge area

28th January


Team 30
25th February



Team 30
25th MarchTeam 30



29th April
Team 30


27th May

Team 30

24th June


Team 30
29th July



Team 30
26th AugustTeam 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

DateTimePresentingRoomContent
16.12.22
No lab meeting - Parasite@York meeting Jeffares lab

06.01.23
No lab meeting - Parasite@York meeting (Kaye lab)

13.01.2311:00KellyWilliamson RoomsLab meeting
20.01.2311:00JoWilliamson RoomsLab meeting
27.01.23
No lab meeting - Parasite@York meeting (Wright lab)

03.02.2311:00Remembering KellyWilliamson Rooms
10.02.2311:00DelphineWilliamson RoomsLab meeting
17.02.23
No lab meeting - Parasite@York meeting (Cayla lab)

24.02.2311:00AdamWilliamson RoomsLab meeting
03.03.2311:00CecileWilliamson RoomsJournal Club
10.03.23
No lab meeting - Parasite@York meeting (Walrad lab)

17.03.2311:00EnricaWilliamson RoomsJournal Club
24.03.2311:00CristinaWilliamson RoomsJournal Club
31.03.23
No lab meeting - Parasite@York meeting (Crosnier lab)

07.04.23
No lab meeting - Good Friday

14.04.2311:00VincentWilliamson RoomsLab meeting
21.04.23
No lab meeting - Parasite@York meeting (Perez Mazliah lab)

28.04.2311:00JoWilliamson RoomsJournal Club
05.05.2311:00DelphineWilliamson RoomsJournal Club
12.05.2311:00No lab meeting - Parasite@York meeting (Fellows)

19.05.2311:00AdamWilliamson RoomsJournal Club
26.05.2311:00CecileWilliamson RoomsLab meeting
02.06.23
No lab meeting - Parasite@York meeting (Faria lab)

09.06.2311:00EnricaWilliamson RoomsLab meeting
16.06.2311:00CristinaWilliamson RoomsLab meeting
23.06.23
No lab meeting - Parasite@York meeting (Wilkinson and Hewiston lab)

30.06.2311:00VincentWilliamson RoomsLab meeting
07.07.2311:00JoWilliamson RoomsLab meeting
14.07.2311:00Delphine   Williamson RoomsLab 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

https://docs.google.com/document/d/11gq-I40QAj32U87i93biUx-08luzeZxrVlfKGScw8IU/edit

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

SAPO licence: https://drive.google.com/file/d/1p7eqnIab5M69Acmiu2KHNVKsg9tL-Aah/view?usp=share_link

Lab PPE

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.

Waste routes

Waste disposal: https://www.york.ac.uk/biology/intranet/health-safety/waste/summary-lab-waste-practices/

Poster: https://drive.google.com/drive/u/1/folders/1Jbkh_uZTvApPQTHe5pbWTPRKcYImo0xU

First aid

First aid room is in biology atrium near mail room.

Fire

Fire sweeper for L1: 

Spills, accidents, incidents and near misses 

Chemical spills: https://www.york.ac.uk/biology/intranet/health-safety/chemical-safety-2/chemicalspillages/

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'.

Competency tables

Last updated: 01/10/2022

Training records can be found from historical electronic copies of this page

TechniquePerson responsibleProtocolRisk assesmentPerformTrain others
AKTA Pure handling (HisTrap purification, column cleaning/regeneration)Cristina

AKTA pure HisTrap purification_clean and recharge

AKTA Pure RA


Cecile, Delphine, Cristina, AdamCecile, Delphine, Cristina, Adam
Avexis screenEnricaAVEXIS  AVEXIS RACecile, Enrica, Cristina, AdamCecile, Enrica
SAVEXISCecileCecile, Adam, Kelly, JoeCecile
Batch his-tag purificationDelphineBatch his-tag purificationBatch His-tag purification RACecile, Delphine, Cristina, Adam, JoeCecile, Delphine, Cristina, Adam
BIAcore handling


Cecile, Enrica, Cristina, AdamCecile
Bioluminescence assay (plate reader)DelphineBioluminescence assay (plate reader)Bioluminescence assay (plate reader) RADelphineDelphine
Blood smearsDelphineBlood smearsBlood smears RADelphineDelphine
Changing gas cylindersAdamGas protocolsGas RAAdamDavid Nelson
DNA gel electrophoresis (agarose/EtBr/SybrSafe)JoeDNA ElectrophoresisDNA Electrophoresis RAAdam, Cecile, Delphine, Enrica, Cristina, Vincent, Kelly, JoeAdam, Cecile, Delphine, Enrica, Cristina, Vincent, Kelly, Joe
DNA/plasmid prepJoePlasmid PreparationPlasmid Preparation RAAdam, Cecile, Delphine, Enrica, Cristina, Vincent, Kelly, JoeAdam, Cecile, Delphine, Enrica, Cristina, Vincent, Kelly, Joe
ELISA (BIO-proteins)CecileAdam, Cecile, Delphine, Enrica, Cristina, Kelly, JoeCecile, Enrica, Delphine
EZ-linked biotinylationCecileEZ-link biotinylation protocol.docx


Adam, CecileCecile
Flow cytometry



Adam, Enrica, VincentTraining provided by TF staff
Freezing/thawing cellsEnricaProtocolFreezing/Thawing cells_RAAdam, Cecile, Delphine, EnricaCecile, Enrica, Adam
Fumigating hoodsCristinaProtocol


HEK293 (E, F, 6E) cell culture (incl. transfection)Enrica

Bio-safety RA

HEK293 Cell culture_RA

Adam, Cecile, Delphine, Enrica, Cristina, Vincent, Kelly, JoeCecile, Enrica, Kelly
Hybridoma generation (fusion, culture, screen)Cecile

CecileCecile
I.P. injection mouseDelphineI.P injectionN/A (refer to BSF RA)Cecile, Delphine, Enrica-
ImmunofluorescenceAdamProtocolImmunofluorescence RADelphine, Enrica, AdamEnrica
Incubator cleaningCristinaProtocol


In vitro fertilisation (mouse)EnricaN/A (refer to BSF RA)EnricaEnrica
Insect cell culture and transfectionVincentSf21 insect cell cultureCulture and freeze/thawing of cell lines_Protocol_RACristina, VincentCristina, Vincent
IVISDelphineIVIS imagingN/A (refer to BSF RA)DelphineDelphine
Leishmania cultureAdamLeishmania RAAdamAdam
Lentivirus production/ transductionAdam

Production

Transduction

Lentivirus RAAdamAdam
Magnetic beads purificationAdamMagnetic beads purification RAAdam, DelphineAdam
Microbiology hood cleaning
Protocol


Mouse oocyte harvestingEnricaMouse oocyte harvestingN/A (refer to BSF RA)Enrica-
Myeloma/hybridoma cell cultureCecile

CecileCecile
OX68 expression and purificationGavinProtocolOX68 purification RA

Parasite isolation from bloodDelphine

Collecting blood using cardiac puncture

Parasite isolation from blood

Parasite isolation RADelphineDelphine
PCR/DNA digest/ligationVincent

PCR RA

Restriction digest RA

ligation RA

Adam, Cecile, Enrica, Cristina, Vincent, KellyAdam, Cecile, Enrica, Cristina, Vincent, Kelly
Percutaneous infection (mouse)CecileCecile-
Plasmid data upload to lab databaseEnricaN/AEnrica, Adam, Cecile, KellyEnrica, Adam, Cecile
Plasmid transformation of competent E. coliKellyAdam, Cecile, Delphine, Enrica, Cristina, Vincent, Kelly, JoeAdam, Cecile, Delphine, Enrica, Cristina, Vincent, Kelly, Joe
Prey normalisation (beta lactamase)EnricaPrey normalisationPrey normalisation_RACecile, Enrica, CristinaCecile, Enrica
Preparing chemically competent bacteriaCristinaPreparing competent cells_RACristinaCristina
Protein concentration quantificationCristinaProtein concentration quantificationProtein concentration quantification_RACecile, Delphine, Enrica, Cristina, Adam, Kelly, JoeCecile, Enrica
Protein dialysis/concentrationCecile

Cecile, Delphine, Enrica, AdamCecile, Enrica, Adam
Protein pressCecileCecile, CristinaCecile
SDS-PAGEVincentSDS-PAGE protocolSDS-PAGE RAAdam, Cecile, Delphine, Enrica, Vincent, Kelly, JoeAdam, Cecile, Delphine, Enrica, Vincent, Kelly, Joe
CoomassieVincentCoomassie staining protocolCoomassie staining RAAdam, Cecile, Delphine, Enrica, Vincent, Kelly, JoeCecile, Enrica, Adam, Kelly, Joe
Subcutaneous injection mouseDelphineN/A (refer to BSF RA)Delphine
Size exclusion chromatographyCristinaSuperdex™ 200 Increase 10/300 chromatographySize exclusion and AKTA Pure RA


Cecile, Cristina, AdamCecile, Cristina, Adam
Tissue cultureCristinaProtocol

Bio-safety RA

HEK293 Cell culture_RA

Adam, Cecile, Delphine, Enrica, Vincent, Joe, KellyAdam, Cecile, Delphine, Enrica, Vincent, Kelly, Joe
Western blotVincentWestern blotting RAAdam, Cecile, Delphine, VincentCecile, Enrica, Vincent, Adam
I.V injectionDelphineN/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/Avector1_C819_Mero-bio (no insert)V
N/AC820type II signalpeptide-bio-linker-Cd4V
v1_SP-HLBio-Cd4p1943_E668type II signalpeptide-his-linker-bio-Cd4V75
N/AC821Cd4-COMP-beta-lac*V
v2_Cd4-BioLHp0821_D725rat CD200 - Cd4- bio-linker-his

V64

v4_mero-Cd4-COMPBLFHV087_MTRAP_M770Mero (MTRAP) - Cd4-COMP-beta-lac-3xFLAG-His*V87
v3_mero-Cd4-BioLHI078Mero (RH1) Cd4-bio-Linker-his*V74
_v6_mero-BioLHP3054_Q942Mero (RH5-N-term)-bio-Linker-his* (no Cd4)V
v5_Cd4-COMPBLFHN/A- Cd4-COMP-beta-lac-3xFLAG-His*V

Computing


R-drive connection

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. 

\\storage.york.ac.uk\biology

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

Social media

The Wright Lab Facebook group can be found on the following link - please sign up! https://www.facebook.com/groups/357803710988905

Equipment info

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:

  1. Press DIAG then ENG
  2. Key in 1973 press ENTER
  3. Tab down to
  4. USER ACCESS CODE press ENTER
  5. Then press RESET
  6. 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.


Technology Facility

To register:

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. 


Contacts

Security01904323333 or 3333 from campus phone
Dr Christoph Baumann

Christoph.baumann@york.ac.uk

L1 Safety

Dr James Foxjames.fox@york.ac.ukFacilities
Dr Marie-Christine Labarthe-Last CL2/CL3 lab manager

Lucy Hudson

lucy.hudson@york.ac.uk

Facilities

David Nelsondavid.nelson@york.ac.ukExt. 8524
University H&S services
Ext. 2020
Emergency
Ext. 3333








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