1. What are the components of the GEXSCOPE single-cell RNA library kit?
The GEXSCOPE® Single Cell RNA library Kit consists of seven components, including SCOPE-Chip®, barcoded beads, lysis buffer, Tissue Preservation & Dissociation mastermix, amplification reagents, library construction reagents and adapters. The kit can be ordered as 2 reactions (2RXN) or 16 reactions (16RXN). Depending on the starting material, it can be ordered as Tissue Kit (including tissue preservation and dissociation mastermix), or as Cell Kit.
2. What is the difference between the Tissue Kit and Cell Kit?
The Tissue Kit has two more components than the Cell Kit: it contains the sCelLiVE® Tissue Preservation Buffer and the Tissue Dissociation Mastermix.
3. What tissue types are suitable for the GEXSCOPE single cell RNA library kit?
The GEXSCOPE® Kit has been tested and verified on more than 300 types of tissues, mostly in human and mouse. These include (but are not limited to) lung, stomach, intestine, liver, ovary, prostate, breast, glioma, lymph node, kidney, testis, placenta, thymus, spleen, embryo, neuroblastoma, pituitary gland, skin, pancreas, PDX mice and more. Please contact your account manager for our detailed list of verified sample types.
4. How effective is the sCelLiVE™ Dissociation Mastermix in dissociating needle biopsy samples?
The sCelLiVE®Dissociation Mastermix has been tested and verified on more than one thousand needle biopsy samples obtained directly from cancer patients. In general, we recommend to start with 3-5 pieces of needle biopsies (containing about 50,000-100,000 cells). The cell viability can reach >90% in the sCelLiVE preservation buffer for up to 3 days.
5. What are the recommended quality control standards for successful single cell suspensions?
We recommend to use cell suspensions with a cell viability >80% and a total of >20,000 cells.
6. What are the effects of too many red blood cells on subsequent experiments?
Too many red blood cells will affect the quality of data. It is recommended to use red blood cell lysis solution to remove red blood cells.
7. How do Barcoded Beads capture the mRNA?
The Poly(T) of barcoded beads bind with the 3’ polyA-tail of mRNA to capture mRNA.
8. How long are the cell barcode and UMI?
Cell Barcode is 24bp, UMI is 12bp.
9. How many probes are on one bead? Do you sell beads alone?
There are about 108 probes on the same bead. We do not sell beads alone.
10. What are the different configurations for the SCOPE™-chip:
The SCOPE-chips have several configurations: the standard chip has 150,000 microwells on one chip and can capture up to 10,000 cells at a time; the high density chip (HD) has 250,000 microwells on a chip and can capture up to 30,000 cells at a time. The Dual-well (DW) chip has microwells with a larger diameter to capture larger cells (up to 100µm) and cells with irregular morphology.
11. What is the sample throughput of the Matrix™ system?
Currently, the Matrix instrument V1.0 can hold 1-2 chips per run. On each chip uo to 30,000 cells can be captured. Sample multiplexing of up to 16 samples is possible through our CLindex sample multiplexing kit.
12. What is the cell capturing rate for SCOPE-chip?
The cell capturing rate is about 35%- 65% on our SCOPE-Chips. We recommend to load around 10,000 cells for our standard SCOPE-chip and 30,000 cells for our high density chip.
13. How is the doublet rate for the SCOPE-chip?
Doublets are defined as two or more than two cells in the same microwell. Please see figure below for a statistic of our doublet rate:
14. What is the recommended sequencing depth per cell?
The sequencing depth varies depending on the research purpose. In most cases, we recommend a sequencing depth around 50,000 reads/cell. However, we can adjust the sequencing depth ranging from 20,000 reads/cell to 100,000 reads/cell.
15. How do I process the single cell sequencing data generated by SCOPE-chip?
We developed an automatic analysis software CeleScope® to process the single cell sequencing data generated by our technology. The software can be downloaded for free at: https://github.com/singleron-RD/CeleScope.
The automatic pipeline includes steps for cell barcodes extraction, correction, alignment, read counting and gene expression matrix generation. An html report is also provided to the users, containing QC metrics for each analysis step.
16. Do you sell sCelLiVE tissue preservation buffer and tissue dissociation mastermix stand-alone?
No. The sCelLiVE tissue preservation buffer and tissue dissociation mastermix are included in our (tissue) library kit. We do not sell them stand-alone.