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Christmas tissue culture rota

DatePersonCells
Monday 19th DecKelly6E,F
Wednesday 21st DecCristina6E,F
Friday 23rd DecCristina6E,F
Monday 26th DecCecile6E,F,insect
Wednesday 28th DecAdam6E, F, Insect
Friday 30th Dec

Kelly

6E,F

Monday 2nd JanCecile6E,F,insect
Wednesday 4th JanCristina6E,F



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
16.09.2211:00JarrodB/K/157ALab meeting
23.09.2211:00CecileWilliamson RoomsJournal Club
30.09.2211:00EnricaWilliamson RoomsJournal Club
07.10.2211:00

Cristina

Williamson RoomsJournal Club
14.10.2211:00VincentWilliamson RoomsLab meeting
21.10.2211:00DelphineWilliamson RoomsLab meeting
28.10.2211:00AdamWilliamson RoomsJournal Club
04.11.22
No lab meeting - Parasite@York meeting

11.11.2211:00

Cecile

Williamson RoomsLab meeting
18.11.2211:00EnricaWilliamson RoomsLab meeting
25.11.2211:00No lab meeting - Parasite@York meeting

02.12.2211:00CristinaWilliamson RoomsLab meeting
09.12.2211:00VincentWilliamson RoomsJournal Club
16.12.22
No lab meeting - Parasite@York meeting

06.01.23
No lab meeting - Parasite@York meeting

13.01.2311:00KellyWilliamson RoomsLab meeting
20.01.2311:00JoWilliamson RoomsLab meeting
27.01.23
No lab meeting - Parasite@York 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
SAVEXISCecile
Cecile, AdamCecile
Batch his-tag purificationDelphineBatch his-tag purification
Cecile, Delphine, Cristina, AdamCecile, Delphine, Cristina, Adam
BIAcore handling


Cecile, Enrica, Cristina, AdamCecile
Bioluminescence assay (plate reader)Delphine

DelphineDelphine
Blood smearsDelphine

DelphineDelphine
Chemical deglycosylation of proteins




DNA gel electrophoresis (agarose/EtBr/SybrSafe)JoeDNA ElectrophoresisDNA Electrophoresis RAAdam, Cecile, Delphine, Enrica, Cristina, VincentAdam, Cecile, Delphine, Enrica, Cristina, Vincent
DNA/plasmid prepJoePlasmid PreparationPlasmid Preparation RAAdam, Cecile, Delphine, Enrica, Cristina, VincentAdam, Cecile, Delphine, Enrica, Cristina, Vincent
ELISA (BIO-proteins)Cecile
Adam, Cecile, Delphine, Enrica, CristinaCecile, Enrica, Delphine
EZ-linked biotinylationCecileEZ-link biotinylation protocol.docx



Adam, CecileCecile
Flow cytometry



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


HEK293 (E, F, 6E) cell culture (incl. transfection)Enrica
Adam, Cecile, Delphine, Enrica, Cristina, VincentCecile, Enrica
Hybridoma generation (fusion, culture, screen)Cecile

CecileCecile
I.P. injection mouseDelphineI.P injection
Cecile, Delphine, Enrica-
ImmunofluorescenceAdamProtocol
Delphine, Enrica, AdamEnrica
Incubator cleaningCristinaProtocol


In vitro fertilisation (mouse)Enrica
EnricaEnrica
Insect cell culture and transfectionVincent

Cristina, VincentCristina, Vincent
IVISDelphineIVIS imaging
DelphineDelphine
Leishmania cultureAdamLeishmania RAAdamAdam
Lentivirus production/ transductionAdam

Production

Transduction

Lentivirus RAAdamAdam
Magnetic beads purificationAdam
Adam, DelphineAdam
Microbiology hood cleaning
Protocol


Mouse oocyte harvestingEnricaMouse oocyte harvesting
Enrica-
Myeloma/hybridoma cell cultureCecile

CecileCecile
OX68 expression and purificationGavinProtocol


Parasite isolation from bloodDelphine

Collecting blood using cardiac puncture

Parasite isolation from blood


DelphineDelphine
PCR/DNA digest/ligationVincent



Adam, Cecile, Enrica, Cristina, VincentAdam, Cecile, Enrica, Cristina, Vincent
Percutaneous infection (mouse)Cecile
Cecile-
Plasmid data upload to lab databaseEnrica


N/AEnrica, Adam, CecileEnrica, Adam, Cecile
Plasmid transformation of competent E. coliKellyAdam, Cecile, Delphine, Enrica, Cristina, VincentAdam, Cecile, Delphine, Enrica, Cristina, Vincent
Prey normalisation (beta lactamase)EnricaPrey normalisation
Cecile, Enrica, CristinaCecile, Enrica
Preparing chemically competent bacteriaCristina



CristinaCristina
Protein concentration quantificationCristina

Cecile, Delphine, Enrica, Cristina, AdamCecile, Enrica
Protein dialysis/concentrationCecile

Cecile, Delphine, Enrica, AdamCecile, Enrica, Adam
Protein pressCecile
Cecile, CristinaCecile
SDS-PAGEVincent

Adam, Cecile, Delphine, Enrica, VincentAdam, Cecile, Delphine, Enrica, Vincent
CoomassieVincent

Adam, Cecile, Delphine, Enrica, VincentCecile, Enrica, Adam
Subcutaneous injection mouseDelphine
Delphine
Size exclusion chromatographyCristinaSuperdex™ 200 Increase 10/300 chromatographySize exclusion and AKTA Pure RA


Cecile, Cristina, AdamCecile, Cristina, Adam
Tissue cultureCristinaProtocol
Adam, Cecile, Delphine, Enrica, Vincent, JoeAdam, Cecile, Delphine, Enrica, Vincent
Western blotVincent



Adam, Cecile, Delphine, VincentCecile, Enrica, Vincent, Adam
I.V injectionDelphine
Delphine


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-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

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 annotatoin spreadsheet: https://docs.google.com/spreadsheets/d/171nm31wC6oCVllNdCmYio-hjG92wqI5N/edit#gid=1111209947

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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