10x Self-Service for internal Users

OGC Single Cell walk-up self-service facility

OGC offers a self-service facility for 10x users from Wellcome Centre for Human Genetics (WHG) to access the 10x Chromium Controller upon advance booking. Apart from the 10x Chromium and the associated equipment (see below list), our procedural room is equipped with a Luna-FX7 automated fluorescence cell counter for accurate and robust quantification to guide the loading of your cell or nuclei samples on the Chromium chip.

Our 10x self-service facility is equipped with:

  • 10x Chromium controller
  • Luna-FX7 automated cell counter – This instrument is only open for the purpose of preparing a 10x run (i.e. optimisation, final QC before loading), and will require advance booking of the facility
  • Vortex mixer with 10x Vortex Adapter
  • Vortex mixer
  • Chromium NextGEM Secondary Holder
  • 10x Magnetic Separator
  • Eppendorf Master Cycler Nexus Flexlid
  • Mini Centrifuge (for 8-tube strip, and for 1.5ml Eppendorf)
  • Pipette – multichannel P20, P200
  • Pipette – P2, P20, P200, P1000
  • Fridge and -20ºc freezer (for temporary storage only)




To minimise the risk of contamination, we do not recommend sharing of reagents or consumables between users. Therefore, we expect individual users to provide their own reagents and consumables including all plastics and make sure that they are GEM-safe.

Click the button below to the official 10x Genomics website, select your 10x workflow and click on “Library Prep” to download the correct user guide, and make sure that you have all the reagents**, consumables, and equipment before your 10x run date.

10x Workflow

Click the button below for additional 10x validated suppliers for emulsion-safe plastic consumables.

10x Validated Suppliers

**Optimisation of single cell/ single nuclei suspension samples can often take several weeks or months, and some of the 10x reagents tend to have relatively short shelf-life. Therefore, we recommend users to have their cell/nuclei prep fully optimised before purchasing the 10x products.



How to access the OGC Single Cell walk-up self-service facility

If you are based in WHG, there are 4 easy steps you can gain access to the OGC 10x self- service facility.

Step 1

Register and Training

All users will require basic training from OGC staff before they may run the 10x Chromium unaided. Training will take place at the Wellcome Centre where the self-service facility is based, and will involve the use of the official 10x Chromium Controller Training Kit to familiarise new users with the essential techniques required to perform the most commonly used 10x workflows. The cost of training will be £450.94 per user. Only trained users will be authorised to access the facility.

You can request training information by contacting ogc-walkup@well.ox.ac.uk

Step 2

Booking Run Slot

We use ARIA, developed by the Division of Structural Biology at Oxford University (STRUBI) as the booking platform for this service. Create an ARIA user account by following the step by step instructions here: ARIA booking system

Once you have registered, e-mail ogc-walkup-singlecell@well.ox.ac.uk to let us know and we will add you to the list of users. Booking slots are 1 day (24hrs) each for the exclusive access to the Single Cell walk-up self-service facility (regardless of which instrument you require). In order to book a one-day slot (£101.50 per slot, Feb 2022), you will need to raise a purchase order (PO) number.

Each booked run slot will be billed irrespective of whether or not it is used. WHG members can raise a PO without a quote, please raise a PO for the number of one-day slots required in advance of booking the run. Booking can be made up to 1 week in advance. Bookings made beyond this period may be subject to cancellation for operational reasons.
A run slot may be cancelled without charge up to 2 days before the slot.

Logon to ARIA, view the calendar for availability, and request a run slot. Provide a PO number for payment and submit. You will be notified within 1 working day that your run slot is approved or if there is a problem. If you need to book a run less than 1 day in advance, please e-mail ogc-walkup-singlecell@well.ox.ac.uk to notify us of the booking.

At the end of each month, usage will be recharged to the appropriate PO number. In the first instance, no formal restriction will be placed on the number of run slots that can be booked and it is hoped that internal users will work together to ensure fair and optimal usage.

Step 3

Running single cell/ single nuclei samples on 10x Chromium

Please note that this is an unsupported self-service for users who have received a one-off standardised training from OGC staff and are authorised to access the facility. 10x reagents are expensive. Self-service users are recommended to be relatively experienced, competent, and familiar with the concept of the relevant 10x applications, esp in the case of the 10x multiomics workflow.

The 10x Genomics website/blog contains comprehensive information required to perform a successful run. Please go to https://support.10xgenomics.com to find the relevant information for your project. If you are still in doubt after going through the official 10x materials by yourself, please feel free to reach out to one of our project managers who will try their best to point you to the right direction. However, due to a high demand for full-service 10x runs, we will prioritise for our full-service users.

Cell/ nuclei quantification:

Our Single Cell walk-up self-service lab is equipped with the LUNA-FX7TM automated cell counter for rapid and accurate quantification of cells or nuclei to guide your loading onto the Chromium NextGEM chip. Please read the official Luna-FX7 user manual thoroughly before use. Please provide your own reagents, such as AO/PI cell viability dye (F23001, Labtech) and LUNA 8-channel slides (L72001, Labtech).

Our 10x self-service facility is designed to support users to perform their 10x run (i.e. GEM generation on the Chromium, transferal of GEMs and GEM-RT incubation), we expect users to perform subsequent steps in their own lab so that other users may access the Chromium Controller with minimal interference or risk of contamination. In any case, please restrict access to only the day(s) that you have booked.

Step 4

Sequencing of premade library pools

Once you have constructed, indexed, and pooled your 10x libraries, please refer to our guidelines for the requirements for submitting pre-prepared library pools to the OGC for sequencing. Please email one of our project managers at genomicsinfo@well.ox.ac.uk to complete the required paperwork. Your library pool will be QC’d and sequenced on a standalone sequencing platform. Once sequenced, data will be demultiplexed using cellranger mkfastq and standard FASTQ files delivered via an FTP link. We also deliver an interactive report that provides a summary of all cellranger count QC metrics, automated cell clustering analysis (t-sne and UMAP), and classification of 68 cell types defined by the transcriptomic signature data based on the Human Cell Atlas study.

Sequencing of premade library pools