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Emergency

For fire or first aid dial "3333"

Security: dial "4444"

Contents

Lab Databases

-80C Freezer: https://docs.google.com/spreadsheets/d/1bVso3jVDVib9qjp6jOiTl6bjtuIGMTBX6k10DHl3u1o/edit?usp=sharing

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

Useful Links

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

VAT exemption certificate: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/725978/Certificate-A-701-6.pdf

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/

Unigreen: selling old equipment, buying secondhand: https://docs.google.com/document/d/1W5Dm4--AkirfomX07OLoIAdU7XiIDMSRdABR2Ju2KYg/edit

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

Cleaning rota for L1 communal lab areas

Last updated: 03 Mar 2022 

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

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

CO2 pipeline and handing:  https://docs.google.com/document/d/1JL7sAXvVOcx1lhiIzc37QHdr2QlTznQQ/edit

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

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 

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.  

To read the barcode on the small tubes in the library plug the Honeywell scanner into a USB port in your computer, open any word processing program and scan the barcode. The barcode number that will appear is the Tube_ID in the google doc spreadsheet.

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

Alphafold

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