Sample types compatible with the workflow
Below you can find the sample types that Single Cell Discoveries accepts for running Parse Biosciences WT scRNA-seq workflows. Please do not hesitate to reach out to us in case you have additional questions.
- Cryopreserved (cells) – we thaw the cells and perform QC before fixing the cells using the Evercode Cell Fixation V3 protocol.
- Note: it is advised to send us one extra vial for QC purposes. We can use this to check the cell concentration and viability prior to starting the actual experiment. If we discover a problem with the sample (e.g. cell number too low, or clumpy cells) there is still an opportunity to reach out and discuss the best next steps.
- Snap frozen tissue – we perform nuclei extraction and fix the nuclei using the Evercode Nuclei Fixation V3 protocol.
- Fixed samples – only when fixed with the kits provided by Parse Biosciences and stored according to the instructions in the protocol.
- Samples must be fixed with official Parse Biosciences fixation kits, either by using Evercode Cell Fixation v3 when working with cells or Evercode Nuclei Fixation v3 when working with nuclei. Samples fixed using different protocols or fixatives might not be compatible with the downstream library preparation.
- Fixed samples can be stored at -80°C for up to 6 months.
- It is advised to send us one extra vial for QC purposes. We can use this to check the cell concentration and quality of the single cell/nuclei suspension prior to starting the actual experiment. If we discover a problem with the sample (e.g. cell/nuclei number too low, excessive clumps or debris) there is still an opportunity to reach out and discuss the best next steps.
Required Cell viability prior fixation > 70%
We strongly advise to only proceed with fixation of samples that have over 70% viable cells. If you know or are concerned that your cells viability is under 70%, please contact us to discuss the best way to proceed.
Number of cells/nuclei
Depending on the targeted number of cells per sample, different cell numbers will be required as starting material.
- For targeting 10.000 cells/nuclei (Evercode WT Mini)
- The maximum number of samples is 12.
- The total input number of cells/nuclei (across all samples) is 60.000*
- For targeting 100.000 cells/nuclei (Evercode WT)
- The maximum number of samples is 48.
- The total input number of cells/nuclei (across all samples) is 500.000*
- For targeting 1M cells/nuclei (Evercode WT Mega)
- The maximum number of samples is 96.
- The total input number of cells/nuclei (across all samples) is 3,75M*[*] Important note: this cell number does not account for cell loss during thawing, washing and cell counting.
For tissue samples the same numbers apply to the number of nuclei that need to be extracted for each respective kit. As the numbers of nuclei can vary between different tissue types a pilot might be needed if the necessary nuclei numbers are not reached.
Our standard minimum input for nuclei extractions is 50 mg of tissue.
Shipment
Samples should be shipped in a Styrofoam box with enough dry ice. Please check our shipping section for more information.