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For fire or first aid dial "3333"

Security: dial "4444"


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

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)


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


Contents

Useful contacts and Links


Lone worker policy: https://www.york.ac.uk/biology/intranet/health-safety/lone-working/#tab-4

Good lab practice: https://www.york.ac.uk/biology/intranet/health-safety/code-lab-standards/

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


Security01904323333 or 3333 from campus phone
Dr Christoph Baumann

Christoph.baumann@york.ac.uk

L1 Safety
Dr James Fox
Facilities?
Dr Marie-Christine Labarthe-Last marie-christine.labarthe-last@york.ac.ukCL2/CL3 lab manager
Lucy Hudson
Facilities?


Lab responsibilities

Last updated: 17/09/2021

AdamUnderbench -80 freezer, Enzymes (PCR, RE), pH meter, molecular biology, gel tanks, CL3 protocols and handbook regular revision reminders, passport updates
CecileElectronic and physical repository (databases, plasmids), tissue culture room fridge
EnricaHome Office regulated procedures database, microscopes
DelphineFreezers, Lab meeting rota
JarrodBIAcore, BIAcore fridge
Cristina

Orphaned

jobs

Ordering, health and safety local co-ordinator, monthly safety check, cell lines, thawing fresh 293 cells, protein press, flask cleaning rota, plate reader, keep incubator water reservoirs full

AKTA Xpress, Pures, recharging Ni2+ columns


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
25.02.2211:00No lab meeting

04.03.2211:00CecileB/K/157AJournal Club
11.03.2211:00EnricaB/K/157AJournal Club
18.03.2211:00

No lab meeting 

Parasites @ York meeting



25.03.2211:00No lab meeting - BSP meeting

01.04.2211:00CraigB/K/157ALab meeting
08.04.2211:00JarrodB/K/157ALab meeting
15.04.2211:00No lab meeting - Good Friday

22.04.2211:00

No lab meeting 

Parasites @ York meeting



29.04.223:30AdamB/M/023Lab meeting
06.05.2211:00DelphineB/K/157ALab meeting
13.05.2211:00CecileB/K/157ALab meeting
20.05.2211:00

No lab meeting 

Parasites @ York meeting



27.05.2211:00EnricaB/K/157ALab meeting
03.06.2211:00No lab meeting

10.06.2211:00CristinaB/K/157ALab meeting
17.06.2211:00

No lab meeting 

Parasites @ York meeting



24.06.2211:00T.B.D.

Williamson Rooms

Lab meeting
01.07.2211:00AdamB/K/157ALab meeting
08.07.2211:00DelphineB/K/157ALab meeting


Travelling - fill out travel log for insurance: https://www.york.ac.uk/staff/working/insurance/

HEALTH AND SAFETY

Last updated: 18/10/2021


Risk assesments and SOP's and general safety

York H&S web site: https://www.york.ac.uk/biology/intranet/health-safety/

York H&S forms / training / near miss reporting: https://www.york.ac.uk/admin/hsas/index.html


Hard copies of Risk Assessments and training records are kept in the lab.

DEPARTMENTAL HEALTH & SAFETY ADVISOR (Dr David Nelson / F0 / Ext 8524)
UNIVERSITY HEALTH & SAFETY SERVICES (Ext 2020)
EMERGENCY / SECURITY SERVICES (Ext. 3333)

Safety monitor for L1 is Christoph Baumann: https://www.york.ac.uk/media/biology/documents/infrastructure/hs/SafetyMonitorsList.pdf 

Fire sweeper for L1

First aid room is in biology atrium near mail room.

Lone working policy: https://www.york.ac.uk/biology/intranet/health-safety/lone-working/#tab-4

Good lab practice: https://www.york.ac.uk/biology/intranet/health-safety/code-lab-standards/

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

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


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.



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.  If you need to 

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'.




OligoFinder link: http://intweb.sanger.ac.uk/cgi-bin/teams/team30/oligo_finder2.pl

Plasmid Atlas link: https://www.dna20.com/eCommerce/tools/plasmid-mapper

Plasmid database link: http://web-wwwtomcatlive-03.internal.sanger.ac.uk:8001/login

For booking your flasks of HEK293-6E cells, please use the following link to fill out the booking form. - https://forms.gle/MJFoMqixUgkp6FUt9


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/

TECHNOLOGY FACILITY

To register here is how:

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. 


COMPETENCY TABLES

Last updated: 18/12/2019

The electronic version can be found in the Team 30 shared drive in the Health and Safety folder. Paper copies can be found in the lab training folder.

TechniquePerformTrain
AKTA express handlingCecile, Delphine, Enrica, Francis, Nicole, SumanaCecile, Enrica, Francis, Nicole
AKTA Pure handlingCecile, Delphine, Francis, NicoleFrancis, Nicole
Avexis screenCecile, Enrica, Francis, SumanaCecile, Enrica, Francis, Sumana
BIAcore handlingCecile, Enrica, Francis, NicoleFrancis
Bioluminescence assay (plate reader)Francis, DelphineFrancis
Blood smearsFrancis, DelphineDelphine
CellomicsSumana
cancer cell cultureFrancis, Nicole, SumanaSumana
cancer cell screeningFrancis, SumanaSumana
Chemical deglycosylation of proteinsFrancisFrancis
Culling mice schedule 1Adam, Cecile, Enrica, Francis-
DNA gel electrophoresis (agarose/EtBr)Adam, Cecile, Delphine, Enrica, Francis, Nicole, SumanaCecile, Enrica, Francis, Nicole, Sumana
DNA/plasmid prepAdam, Cecile, Delphine, Enrica, Francis, Nicole, SumanaCecile, Enrica, Francis, Nicole, Sumana
ELISA (BIO-proteins)Cecile, Delphine, Enrica, Francis, Nicole, SumanaCecile, Enrica, Francis, Nicole, Sumana
Erythrocyte binding assaySumanaSumana
EZ-linked biotinylationCecile, FrancisCecile
Flow cytometryAdam, Enrica, Francis, Nicole, Sumana-
Freezing/thawing cellsAdam, Cecile, Delphine, Enrica, Francis, Nicole, SumanaCecile, Enrica, Francis, Nicole, Sumana
HEK293 (E, F, 6E) cell culture (incl. transfection)Cecile, Delphine, Enrica, Francis, Nicole, SumanaCecile, Enrica, Francis, Nicole, Sumana
Hybridoma generation (fusion, culture, screen)Cecile, NicoleNicole
I.P. injection mouseCecile, Delphine, Enrica, Francis-
ImmunofluorescenceDelphine, Enrica, Francis, SumanaEnrica
Intracardiac punctureDelphine-
In vitro fertilisation (mouse)EnricaEnrica
I.V. injection mouse
-
IVISDelphineDelphine
Leishmania culture

Lentivirus production/ transductionAdam, SumanaSumana
Magnetic beads purificationAdam, Delphine, Francis
Mouse oocyte harvestingEnrica-
Myeloma/hybridoma cell cultureCecile, NicoleNicole
Parasite isolation from bloodDelphine
PCR/DNA digest/ligationAdam, Cecile, Enrica, Francis, Nicole, SumanaCecile, Enrica, Francis, Nicole, Sumana
Percutaneous infection (mouse)Cecile-
Plasmid transformation of competent E. coliAdam, Cecile, Delphine, Enrica, Francis, Nicole, SumanaCecile, Enrica, Francis, Nicole, Sumana
Prey normalisation (beta lactamase)Cecile, Enrica, Francis, Nicole, SumanaCecile, Enrica, Francis, Nicole, Sumana
Protein concentration quantificationCecile, Delphine, Enrica, Francis, Nicole, SumanaCecile, Enrica, Francis, Nicole, Sumana
Protein dialysis/concentrationCecile, Delphine, Enrica, Francis, Nicole, SumanaCecile, Enrica, Francis, Nicole, Sumana
Protein microarray (96-well/slides)Nicole
Protein pressNicoleNicole
qRT-PCREnrica, FrancisEnrica
RNA and cDNA prepCecile, Enrica, Francis, Nicole, SumanaCecile, Enrica, Nicole
SDS-PAGEAdam, Cecile, Delphine, Enrica, Francis, Nicole, SumanaCecile, Enrica, Francis, Nicole, Sumana
CoomassieCecile, Delphine, Enrica, Francis, Nicole, SumanaCecile, Enrica, Francis, Nicole, Sumana
subcutaneous injection mouse
-
SYPRO Orange staining, Azure (Typhoon scanner)Cecile, Francis, NicoleCecile, Nicole
(Transfectoma culture)CecileCecile
Western blotAdam, Cecile, Delphine, Enrica, Francis, Nicole, SumanaCecile, Enrica, Francis, Nicole, Sumana


VECTORS AT GENEART AND TWIST

Last updated: 16/09/2015

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-hisV64
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




L1 Induction and Rules

Updated 11th September 2021 

New Staff/Student Induction for 2021/22 

General Points 

To keep the lab running smoothly, we have a standard operating procedure for all communal  equipment and areas. Keep these areas tidy by cleaning up afterward and putting things back in the same  place and condition as you found them.  

If you are unsure about anything, ASK. It is always better to check before you do it. 

New technicians, UG and PG students, and post-docs should be given a tour of the wet lab area by  one of the current L1 technicians or the L1 Safety Officer BEFORE starting lab work. 

ALWAYS wear a lab coat in the wet lab area. 

Mobile phones should NOT be used in the wet lab area. Always set your mobile to silent mode in  L1 write-up areas. 

The use of headphones in the lab is strongly discouraged. 

NO lab coats or gloves should be worn outside the wet lab area, unless you are transporting  something that requires you to wear these items. DO NOT open doors outside the wet lab area with  a gloved hand. 

UNDERGRADUATE STUDENTS ONLY: All bags and backpacks must be stored in the lockers  located on the landing outside the entrance to L1 corridor. Coat hooks are available in the write-up  areas for jackets, etc

Use of Communal Equipment / Areas 

Lab Consumables (gloves, tissues, pipette tips, blue roll, etc.) 

Microwaves and Heating Blocks 

Centrifuges (Beckman L7 Ultra and Optima TL Ultra, Sorvall and Sigma) 

(https://www.york.ac.uk/biology/intranet/operational-support/centrifuges/ then click on  “Online Booking System” at top right of web page) The details of your centrifuge run(s)  and a valid workorder code must be recorded in the logbook (next to centrifuges). Do not take someone else’s booking without their permission. Any machine found to be  running, but not booked, could be switched off. 

The booking information on the web should be completed as follows: 

automatically recorded. 

Gel-Doc 


Chemicals Room 
Gel Room 
Constant Temperature (CT) Rooms 
Laminar Flow Hood 
Class II Microbial Safety Cabinet 

Waste Disposal 

ALL LAB CONSUMABLE WASTE AND GENERAL WASTE MUST BE DISPOSED OF in  either a clear autoclave bag, a `tiger´ bag, or a black `general waste´ bag (by hand wash sinks  only) depending on its level/type of contamination (see below). Some decontaminated, plastic  lab consumables can be recycled – see below for more information on the L1 Green Impact  recycling scheme. 

RESIDUAL CHEMICAL MATERIAL is defined as a non-hazardous concentration.  Information on Chemical Waste Threshold Levels can be found on a poster in the L1 Chemicals  Room. 

DRY ICE SHOULD NOT BE POURED INTO THE LAB SINKS. Unwanted clean dry ice  should be placed in the blue insulated box located in room L131 so it can be used by other  groups. Dry ice contaminated with organic solvent should be left to sublimate in the fume hood. 


Lab consumables 

o `Tiger´ bags should be used for non-hazardous identifiable lab waste, which does  not require incineration or autoclaving. Black bins containing these bags must be  labelled `Non-Hazardous Identifiable Lab Waste Only´ (labels are available  from Biology Stores) – wire racks should not be used to hold `tiger´ bags. We pay a significant disposal charge for every ‘tiger’ bag removed from the  Department – therefore, these bags should only be used for non-hazardous  identifiable lab waste that cannot be recycled or disposed of in a black `general waste´ bag. L1 has implemented a recycling scheme for some commonly used, plastic  lab consumables, e.g. serological pipettes, 15 ml and 50 ml screw-cap tubes,  micro-well polystyrene plates, polystyrene tubes, and syringes.

Please see Reyme Herman (in Thomas group) for more information about our lab  plasticware recycling scheme. 

o Significant volumes of non-hazardous liquids must NOT be place in the `tiger´ bags. Only residual liquid contamination of waste is allowed. For this reason, all  non-hazardous liquids must be poured down the sink before putting a tube/container in the `tiger´ bag. 

o Items contaminated with biological (human/animal tissue or fluids) or  microbiological/GM agents must NOT be disposed of via these `tiger´ bags.

o Individual groups are responsible for closing and removing full bags in their lab  areas (see next bullet point). The individual group responsible for the weekly L1  Glassware Rota will remove full bags in communal lab areas, i.e. Chemicals  Room, Gel-Doc Room and Gel Electrophoresis Room.  

o L1 lab staff are responsible for closing full `tiger´ bags (3/4 full or < 10 kg) with  cable ties (Biology Stores code SHE6000), labelling with laboratory ID details  (i.e. `L1 Communal´) and placing them near to the ice machine for collection by  the cleaning staff. A supply of the heavy-duty `tiger´ bin bags, ID labels and  cable ties can be found in the Chemicals Room. 

o Uncontaminated pipette tips, or those contaminated with residual chemicals,  must be placed in a `tiger´ bin bag. NOTE: It is recommended that pipette tips  are collected in disposable plastic jars (available from Biology Stores) before  disposal in a `tiger´ bin bag when full. 

o Uncontaminated pipettes, or those contaminated with residual chemicals must be  placed in Bio-Bin `pipette bins´ to avoid puncturing or splitting `tiger´ bags.  Once a Bio-Bin is full, it should be sealed and placed into a `tiger´ bag for  disposal. Individual groups should purchase Bio-Bin pipette bins from Biology  Stores. 

o Empty plastic chemical containers can be put in `tiger´ bin bags (or washed and  recycled, see below).  

o Weigh boats, micro-titre plates, centrifuge tubes, empty FPLC fraction collection  tubes, disposable plastic flasks, petri dishes (no agar or bacterial contamination)  and buffer filtration devices can be placed in `tiger´ bin bags if they are NOT  contaminated with biological/microbiological agents, or they only contain  residual chemical material.  

o All lab tissue and blue roll contaminated with residual chemical material can be  placed in a `tiger´ bin bag. 

o Uncontaminated gloves or gloves contaminated with residual chemicals should  be placed in the `tiger´ bin bag. 

o Polymerised acrylamide gels can be disposed of in these bags. 

o Empty gas canisters should be placed in the box near the ice machine for  recycling. 

o Lab waste (tissue, blue roll, tubes, gloves, pipettes, pipette tips, plasticware, etc.)  contaminated with hazardous concentrations of any chemical should be placed in  large yellow bins. Information on Chemical Waste Threshold Levels can be  found on a poster in the L1 Chemicals Room. 

o These large yellow bins can be purchased from Biology Stores by individual  groups. 

o All `sharps´ waste, glass vials, NMR tubes, glass ampoules and glass Pasteur  pipettes should be disposed of in these bins, NOT the red glass recycling bin (see  below).

o The `sharps´ bin must NOT be filled above the designated level. If the bin is full,  seal the container and replace with a new one. A communal supply of new  `sharps´ bins are stored in room L136 (under the sink). These small yellow bins  can be purchased from Biology Stores. 

o Glass crimp-top HPLC vials must be disposed of in these bins, NOT the red  glass recycling bin (see below). 

o This type of waste disposal bag is not in use on L1 corridor. Please see the L1  Safety Officer if you need to start using these bags. 

Bacterial 

Liquid waste 

o Decontaminate with Virkon™ (final concentration = 1% w/v) for 1 hour (or  alternatively use Presept). Chloros can only be used on glass containers. 

Solid waste 

o Place in a clear autoclave bag and send for autoclaving (see guidelines below). o Where an autoclave bin (rather than a wire rack) is used it should be labelled  'Autoclave Waste Only' (labels available from Biology Stores). 

o Pipettes contaminated with bacterial culture should be placed in a small  autoclave waste bag. They should not be mixed with other solid waste in a large  autoclave bag as there is a risk of puncturing the bag. 

Chemical 
Glass 
Plastic 
Paper and Cardboard 
Glassware 

All research groups on L1 share communal glassware. This glassware is stored in labelled cabinets  along the windows. When you finish using a piece of glassware, you should wash it with soapy  water, rinse well with tap water followed by deionised water (green tap), then place it in the  communal drying oven. Glassware should not be left to dry next to the sinks as this poses a safety  hazard. All lab glassware breakage should be recorded on the sheet posted near the whiteboard. 

Autoclaving: Microbial Waste Disposal and Media Sterilisation 

All research groups are responsible for their own autoclaving. You should discuss the local rules  for autoclaving items with your PI. The following notes are for guidance only. 

Routines for safe disposal of waste 

Waste Disposal and Lab cleaning duties

Memory Aid for Lab Waste Streams

Friday Bins and L1 communal tasks

Rota Google Calendar (TC flasks, Bins, L1 tasks)

TC Room and Flask cleaning

Biology Stores Counter Opening Times -  Monday to Friday - 9:30 - 12:30 & 13:30 - 15:00

Autoclave Facility -  Monday to Friday - Items brought by 10.30 can be picked up on the same day, items brought by 1.30 will be ready the next day *See TC room and flask cleaning for TC flask instructions 

Sterilisation of clean media, plasticware and glass items 

o 100 ml bottle (max. volume = 60 ml) 

o 500 ml bottle (max. volume = 300 ml) 

o 1 liter bottle (max. volume = 650 ml) 

o 500 ml conical flask (max. volume = 250 ml) 

o 1 liter conical flask (max. volume = 600 ml) 

Lone Working in the Research Labs 

If a postgraduate research student or post-doc is working outside normal working hours in the  laboratory, all work must be inherently low risk. A formal risk assessment is required for higher  risk lone working activities. Guidance on lone working in the laboratory can be found on the  departmental website: http://www.york.ac.uk/biology/intranet/health-safety/lone-working/ (excerpts from website below) 

Lone working represents a situation where a person has neither visual nor audible communication  with someone else who can summon assistance in the event of an accident, illness or other  emergency. Lone working can, therefore, include those work activities undertaken both: during  normal departmental working hours (8.00-18.00 weekdays) and outside normal departmental  working hours (includes weekends and holidays when the University is closed).” 

“Supervisors of all lone workers must be satisfied that an individual has received appropriate  training and has the necessary experience before allowing lone working. It is good practice for  those individuals working outside normal working hours to inform a friend or family member of  their location and approximate time of return.” 

Undergraduate Project Student Supervision 

Dr. Christoph G. Baumann 

L1 Safety Officer