The tissue types listed below were tested in-house using:
GEM-X Flex or GEM-X Flex v2 Gene Expression
- Tissue Fixation & Dissociation for GEM-X Flex Gene Expression (CG000783) or
- Chromium Nuclei Isolation Kit (CG000505) followed by the Fixation of Cells & Nuclei for GEM-X Flex Gene Expression (CG000782)
Next GEM Flex Gene Expression
- Tissue Fixation & Dissociation for Chromium Fixed RNA Profiling Demonstrated Protocol (CG000553) or
- Chromium Nuclei Isolation Kit (CG000505) followed by the Fixation of Cells & Nuclei for Chromium Fixed RNA Profiling (CG000478)
Listed below are the cell yields from 25 mg of various mouse and human tissue types (flash-frozen or fresh). Variability of performance may be observed based on sample handling, quality, composition, and other properties.
Best practice is to minimize changes to sample preparation conditions between experiments in a given study to reduce the likelihood of introducing batch effects. For example, we recommend keeping enzymes used during the Tissue Fixation & Dissociation Demonstrated Protocol consistent.
Tissues with Special Considerations
The following tables summarizes tissues having unique guidance at various steps in the Flex workflow.
Mouse
| Tissue | Tissue Fixation & Dissociation* (Flash-frozen tissue) | Tissue Fixation & Dissociation* (Fresh tissue) | Nuclei Isolation** (Flash-frozen tissue) | Nuclei Isolation** (Fresh tissue) | Additional Notes |
|---|---|---|---|---|---|
| Adipose | Not recommended | Not recommended | 3.00E+04 | Not tested | High lipid content in adipose cells prevents cells from pelleting (cells are buoyant). Nuclei isolation recommended |
| Heart | 9.90E+05 | 2.00E+06 | 3.00E+04 | Not tested | Low yield; Tissue Fixation & Dissociation recommended |
| Leukocytes (cell suspension) | NA | NA | NA | NA | See Demonstrated Protocols (CG0000721) for Blood Fixation and Cell Isolation guidance. If working with freshly isolated leukocytes, fix for 16-24h at room temperature (20°C). No greater than 100k cells into Probe Hybridization for optimal performance. |
| Muscle | 4.10E+05 | Not tested | 1.10E+04 | Not tested | Lower than expected yield using Nuclei Isolation Kit. Tissue Fixation & Dissociation protocol is recommended to improve cell yield. |
| Pancreas | 1.80E+06 | 9.20E+05 | 2.70E+05 | 1.90E+04 | Pancreas can be a challenging tissue and variable data quality may be expected. We recommend generating an FFPE block, if working with fresh pancreas is available. See this article for more details. If performing Tissue Dissociation & Fixation, digestion using Liberase TH 1 mg/mL is recommended. No greater than 100k cells into Probe Hybridization for optimal performance. |
| Spinal Cord | 1.50E+06 | Not tested | 2.20E+05 | Not tested | High debris |
| Spleen | 1.40E+07 | 6.30E+06 | 1.20E+05 | 5.30E+05 | Nuclei prone to clumping, Tissue Dissociation & Fixation recommended. Fix for 16-24h at room temperature (20°C). No greater than 100k cells into Probe Hybridization for optimal performance. |
| Thymus | 1.50E+07 | 2.60E+07 | 4.30E+04 | 7.90E+06 | Nuclei are prone to clumping. Tissue Fixation & Dissociation protocol. recommended. |
Human
| Tissue | Tissue Fixation & Dissociation* (Flash-frozen tissue) | Tissue Fixation & Dissociation* (Fresh tissue) | Nuclei Isolation** (Flash-frozen tissue) | Nuclei Isolation** (Fresh tissue) | Additional Notes |
|---|---|---|---|---|---|
| Colon | 4.00E+04 | Not tested | 6.10E+05 | Not tested | Lower than expected yield from 25 mg colon tissue; using >25 mg tissue recommended. |
| Leukocytes (cell suspension) | NA | NA | NA | NA | See Demonstrated Protocols (CG0000721) for Blood Fixation and Cell Isolation guidance. If working with freshly isolated leukocytes, fix for 16-24h at room temperature (20°C). No greater than 100k cells into Probe Hybridization for optimal performance. |
| Colon | 4.00E+04 | Not tested | 6.10E+05 | Not tested | Lower than expected yield from 25 mg colon tissue; using >25 mg tissue recommended. |
| Spleen | 9.60E+06 | Not tested | 6.50E+06 | Not tested | Fix for 16-24h at room temperature (20°C). No greater than 100k cells into Probe Hybridization for optimal performance. |
| Pancreas | 1.78E+06 | Not tested | 9.11E+05 | Not tested | No greater than 100k cells into Probe Hybridization for optimal performance. |
| BMMC (cell suspension) | NA | NA | NA | NA | Fix for 16-24h at room temperature (20°C). No greater than 100k cells into Probe Hybridization for optimal performance. |
Additional Mouse (Healthy) Tested Tissue List
- List of mouse tissue types that were tested in-house for compatibility with Flex.
| Tissue | Tissue Fixation & Dissociation* (Flash-frozen tissue) | Tissue Fixation & Dissociation* (Fresh tissue) | Nuclei Isolation** (Flash-frozen tissue) | Nuclei Isolation** (Fresh tissue) |
|---|---|---|---|---|
| Bladder | 7.00E+05 | Not tested | 1.70E+05 | Not tested |
| Brain (Forebrain) | 1.00E+06 | 7.90E+05 | 7.10E+05 | 3.00E+05 |
| Brain (Cerebellum) | Not tested | 3.10E+06 | Not tested | 5.20E+05 |
| Brain (Whole) | 1.60E+06 | 8.40E+05 | 7.90E+05 | 7.00E+05 |
| Colon | 2.20E+06 | Not tested | 9.80E+05 | Not tested |
| Eye | 1.60E+06 | Not tested | 3.70E+05 | Not tested |
| Intestine | 3.10E+06 | 1.60E+06 | 9.00E+05 | 2.50E+04 |
| Kidney | 2.70E+06 | 2.50E+06 | 1.20E+06 | 1.00E+06 |
| Liver | 1.30E+06 | 5.70E+05 | 1.00E+06 | 2.80E+05 |
| Lung | 2.00E+06 | 3.10E+06 | 7.40E+05 | 3.40E+05 |
| Ovary | 3.20E+06 | Not tested | 1.20E+06 | Not tested |
| Stomach | 2.50E+06 | Not tested | 3.60E+05 | Not tested |
| Testis | 4.20E+06 | Not tested | 8.60E+05 | Not tested |
| Tongue | 1.40E+06 | Not tested | 2.10E+04 | Not tested |
Human Tested Tissue List
* List of human tissue types that were tested in-house and found to perform well with Flex.
| Tissue | Tissue Fixation & Dissociation* (Flash-frozen tissue) | Tissue Fixation & Dissociation* (Fresh tissue) | Nuclei Isolation** (Flash-frozen tissue) | Nuclei Isolation** (Fresh tissue) |
|---|---|---|---|---|
| Jejunum | 1.37E+06 | Not tested | 4.18E+05 | Not tested |
| Lung | 3.40E+06 | Not tested | Not tested | Not tested |
| Kidney | 2.00E+06 | Not tested | Not tested | Not tested |
| Liver | 1.80E+06 | Not tested | 6.60E+05 | Not tested |
| Ileum | 1.40E+05 | Not tested | 2.37E+05 | Not tested |
| Testes | 2.05E+06 | Not tested | 8.08E+05 | Not tested |
| Duodenum | 3.20E+05 | Not tested | 1.28E+05 | Not tested |
| Breast Cancer | 9.60E+05 | Not tested | 9.20E+05 | Not tested |
| Melanoma | 3.18E+06 | Not tested | 5.98E+05 | Not tested |
| Ovarian Cancer | 9.30E+05 | Not tested | 6.93E+05 | Not tested |
| Pancreatic Cancer | 1.78E+06 | Not tested | 9.11E+05 | Not tested |
| Tonsils | 1.76E+07 | Not tested | 5.15E+05 | Not tested |
* Tissue Fixation & Dissociation for GEM-X Flex Gene Expression (CG000783)
** Chromium Nuclei Isolation Kit (CG000505) followed by the Fixation of Cells & Nuclei for GEM-X Flex Gene Expression (CG000782)