Genomics Core Single Cell 10x Genomics Submission

Due to the nature of processing single cell samples, for all 10x Genomics services you must discuss your project with the Genomics Core prior to submission, we cannot offer a walk up service or accept samples that are not discussed in advance.

In the first instance contact the Single Cell Team to discuss details of the cells or nuclei submission.

We ask you to bring your cell suspension in the required concentration. Below is our sample submission requirements.

Workflow	Kit used	Sample Type	Volume loaded (µl)	Volume to submit (µl)	Total Number of Cells loaded	Submit in tubes
10x Single Cell GEX v3.1 (NextGEM)	sc 3'mRNA v3.1	Cells/Nuclei	43	45	800 - 16,000	1.5ml Eppendorf tubes
10x Single Cell V(D)J v2.0 (NextGEM)	sc 5'mRNA v2.0	Cells	39	40	870 - 17,400	1.5ml Eppendorf tubes
10x Single Cell ATAC v1.1 (NextGEM)	sc ATAC v1.1	Nuclei	5	5	775 - 15,400	0.2ml PCR Tubes
10x Single Cell Multiome ATAC + Gene Expression (NextGEM)	sc Multiome	Nuclei	5	5	775 - 15,400	0.2ml PCR Tubes

Cell Suspensions

Samples should be submitted in a clearly labelled tube (see table above) and brought on ice.

It is critically important to optimise your dissociation and counting methods for your particular cell sample, almost all failures we've experienced are due to fewer cells than expected in the initial sample.

It is recommended for any single cell 10x genomics project to consider a pilot experiment prior to a multi-sample project.

For any other questions you might have about cell preparation, counting and sequencing please see our FAQ page.

How to Complete the 10x Submission Form

The submission form has been tricky to navigate historically. Here is the guide how to fill it out. The first few fields are related to which workflow you want your samples to go through.

Workflow: The most standard experiment type in our facility is "10x Single Cell 3' GEX" so if nothing else was specifically mentioned that is the workflow you should choose.
Additional workflows: Can be left blank if additional workflows are not needed. In the drop down menu is our most common additional workflows for example if you need CITEseq/Cell surface Protein information. All additional Workflows need to be discussed with us in advance, please contact us to discuss.
VDJ Amplification: Only relevant if you choose “10x Single Cell V(D)J” in the workflow field. Do you want TCR, BCR or both enrichments?
Ready to sequence:
- No: if you are still submitting samples that you want pooled and sequenced together. You do not need to fill in the sequencing information (sequencer, flowcell type, number of lanes).
- Yes: if you have submitted all your current samples and are ready to sequence. Please contact us and let us know which samples you want pooled. You will have to fill in the sequencing information (sequencer, flowcell type, number of lanes).

The following information is needed if your samples are ready to sequence, otherwise it can be left blank

Sequencer: For 10x Genomics workflows we recommend using NovaSeq 6000 as it produces the best quality of reads.

Flowcell Type: There are four sizes of flowcells to be used on NovaSeq6000, producing different number of reads per lane (see the table below). If you are unsure how many reads you need, see our FAQ page or contact us to seek advice. The table below gives a guide to the relative sizes.

Flowcell Type	Specification in Million Reads per lane	Typical Performance in Million Reads per lane
NovaSeq SP	325-400	450-500
NovaSeq S1	650-800	950-1000
NovaSeq S2	1650-2050	2000-2100
NovaSeq S4	2000-2500	2700-3000

Number of lanes: Strictly connected to flowcell type and your decision about number of reads needed (as for example one lane of S1 flowcell is equal to two lanes of SP flowcell).

The following information is needed:

Species: Information used only for our Multi-Genome Alignment report. If multiple different species used, please make a note in the submission comment section so we are not concerned that sample has been contaminated.
Billing Information: For 10x Genomics library preparation collaboration codes MUST NOT be used. Please contact us prior to your experiment to set up your grant code in the system.
PO Number: Applicable only for commercial users. Leave blank if it does not apply! Resist the temptation to put "N/A" or "None": it will complicate your bills.

Individual sample information:

Name: : please be consistent with what you label on your tube and what you fill on the submission sheet. Have either date and numbers or a continuous number system on tubes and filling in the form so it makes it easy for us to cross reference samples processed and submitted into our system
E.g. if 3 samples are submitted on 3rd May, and 2 samples submitted on 14th June
- Date and numbers use YYMMDD (Year Month Day with no spaces) in the same format
  - 230503_1_Sample_Name
  - 230503_2_Sample_Name
  - 230503_3_Sample_Name
  - 230614_1_Sample_Name
  - 230614_2_Sample_Name
- OR continuous number system
  - 1_sample_Name
  - 2_sample_Name
  - 3_sample_Name
  - 4_sample_Name
  - 5_sample_Name
Concentration: Concentration of cell suspension provided to our facility in [cells/µl].
Volume: Volume of cell suspension provided to our facility in [µl]. Please refer to table above: for example 45µl should be provided when submitting for 3' v3.1 workflow. We will load 43µl
Species: Only necessary if different to value in cell C17.
Reads per cell: This field is optional, but it will help us in advising you on which flowcell to use, and if we notice any inconsistencies.
10x recommended minimum for
- GEX is 20k reads per cell
- ATAC is 25k reads per cell
Submission comments: Anything that needs to be communicated and might be relevant for the experiment like suggestions about pooling before sequencing, type of antibodies used for staining (CITEseq), information about possible low RNA content etc.