How should a schedule a sample submission?
Please email any member of our staff to schedule a run. At least 2 weeks’ notice is preferred.
How should samples be prepared for 3’ and 5’ assays?
For 3’ and 5’ assays, cells should be suspended in PBS/0.04% BSA at a concentration of 1,000-2,000 cells/uL in 1.5mL tubes. A minimum of 50,000 cells or nuclei are preferred to allow for QC and loading.
How should samples be prepared for scATAC or scMultiome assays?
Nuclei should be freshly isolated and at a concentration of 4,000 nuclei/uL in the appropriate nuclei buffer for your isolation method and assay (we can provide 20X nuclei buffer that comes in the library preparation kit). Nuclei should be in either a 1.5mL or 0.2mL tube. 50,000 nuclei is preferred, but we can work with smaller numbers.
How should samples be prepared for the Flex assay?
We can accept flash frozen or fixed tissue, fixed cells, or FFPE preserved tissue. Tissues and cells should be submitted in 1.5mL tubes. FFPE sections (3-5 10um sections) should be submitted in 1.5mL tubes. Tissues should be minced, between 25-37mg. Users should follow 10X guidelines for tissue and cell fixation.
Are there fixation methods available for other assays?
Yes, 10X now has an approved methanol fixation method compatible with 3’ and 5’ assays (including VDJ profiling and CITE-seq). Please reach out to learn more.
What multiplexing methods are available?
On chip multiplexing and cell hashing (using TotalSeq antibody tags) are available for 3’ and 5’ assays. Flex v2 offers multiplexing capabilities with a probe-based assay for fixed mouse and human samples.
Can you sequence my libraries?
We do not have a sequencer. We can pool your libraries with others and send to the HTGC for sequencing on a 10B or 25B NovaSeq X Plus flow cell. You also have the option of retrieving your libraries and sequencing at the provider of your choice.
How long will you keep my finished libraries?
Libraries that will be sequenced by the researcher should be picked up promptly at completion. If we are doing pooled sequencing at HTGC, libraries must be picked up within 1 month of data availability.
How many samples can be run at one time?
A chromium chip holds 8 samples, however in some cases (such as when isolating nuclei) it is best to limit sample handling to 4. Up to 48 samples can be multiplexed in a Flex run, however this may require splitting the samples for probe hybridization. A consultation is required before planning a Flex run.
What if I’m running late?
Guidelines for submission times can be found on the Users page. While we will do our best to accommodate samples submitted more than 30 minutes after an appointment time, we may need to cancel depending on staff schedules. We will not accept samples for 3’ or 5’ after 4pm Monday-Thursday or 1pm on Friday. scATAC and scMultiome samples will not be accepted after 1pm.
Samples can take between 2-4 hours to reach a safe stopping point, followed by a multi-day library preparation and QC process. This requires us to adhere as closely as possible to appointment times.
It is recommended to do a dry run of the cell isolation, sort, etc. if you are unsure of the time required.