School of Biomedical Sciences
The Chinese University of Hong Kong 香港中文大學

Single Cell Omics Core

About us

fire A major upgrade: Single Cell RNAseq v4 GEM-X solutionfire

fire Research works using our services from SCOC can now be found inside the Publication thread below fire

fire Another option for scRNAseq: The single-cell Fixed RNA Profiling (scFRP)-Part Ifire

fire Another option for scRNAseq: The single-cell Fixed RNA Profiling (scFRP)-Part IIfire

fire Single Cell Gene Expression Low Throughput (LT) Solution service package fire

fire Spatial Omics literature databasefire

fire Launch of Single Cell Fix RNA Profiling Solution fire

fire Application Unlocked: Single Cell Fixed RNA Profiling Solution on FFPE Samples fire

The SCOC provides a streamlined, cell-to-sequencing library service package for Single Cell RNA sequencing (scRNA-seq). It is capable to simultaneously profiling of transcriptomes ranging 500 – 10,000 cells in a single experiment. Different indexing systems are designed to label cell, transcript and sample origin in the sequencing library. This enables multiplexing of different sequencing libraries from multiple samples in the same Next Generation Sequencing (NGS) run. Libraries are Illumina-format compatible.

The service provided by SCOC includes an initial sample QC check, following by an evaluation of overall quality of sample for fitness to continue run. Single cells are then encapsulated in thousands of Gel Bead-in Emulsion (GEM) droplets, where cells are lysed and mRNA molecules reverse transcribed into cDNA. cDNA with specific cell barcodes are then pooled together and subjected to subsequent conventional sequencing library preparation. A final QC is performed on the final sequencing library to ensure sound quality for massively-parallel sequencing.

The SCOC welcomes interested PIs for experimental troubleshooting, intellectual advices as well as project discussions / collaborations.


SCOC equipment
  • RWD C100 Automated Cell Counter with fluorescence (Cell viability check and counting)
  • Light Microscope / Hemocytometer (Manuel cell counting)
  • Compact cooling centrifuge
  • 10X Controller (Single cell encapsulation)
  • Chromium iX (Single cell encapsulation)
  • Visium CytAssist (Spatial profiling)
  • PCR workstation
  • PCRs, thermomixer, vortex, plate centrifuge
  • Qubit 4 Fluorometer (DNA/RNA library quantification)
  • NanoString CosMx Spatial Molecular Imager (spatial multiomics single-cell imaging)
  • 3DHistech TMA Master II (create tissue microarray blocks)

Service Workflow

Workflow overview

Workflow Overview

10X Chromium Next GEM Single Cell 3’ Gene Expression Workflow

Next GEM Workflow

Chromium Next GEM Chip:
Next GEM Chip

  • Up to 8 samples per chip processed in parallel
  • 500 to 10,000 cells per channel
  • 18 minutes run time per chip
  • Preferred cell size < 30 µm
  • ~60-65 % cell recovery efficiency

RT, template switching
RT, template switching

Pre-amp PCR
Pre-amp PCR

cDNA quality control
cDNA quality control

Sequencing library preparation
Sequencing library preparation

Sequencing library quality control
Sequencing library Control

Service request

Please contact Dr Joaquim Vong (email: This email address is being protected from spambots. You need JavaScript enabled to view it. / 39430318) for service request, technical enquiry and project discussion.

For service request, please fill in our Sample submission form.

Service fees include: (please enquire)

✓ Package set: From cell to sequencing library
✓ Cell quality and viability check / basic QC
✓ Sequencing library QC and quantification
✓ Intellectual advices (wet / dry lab)
✓ Troubleshooting

× Sequencing NOT included
× Repeated initial sample QC checks might incur extra charges

Output items

A. Sequencing library
B. QC reports for cDNA and sequencing library
C. Indexing information

The final product is a double-stranded cDNA molecule with sequencing adaptors and 3 different indices (10X barcode: cell info; UMI: transcript info; sample index: sample info). The sequencing library quality is evaluated by running into an Agilent 4200 TapeStation System.

10X Barcode
Source: 10X Genomics


Users are required to fill in and sign the “Service Form for Single Cell Omics Core” prior to sample submission

All users MUST declare the nature of sample(s) submitted to SCOC FREE of any bio-hazardous material.

An initial assessment of cell quality will be conducted for the generation of data with optimal quality. Users may take the risk of sub-optimal data quality if the initial cell quality check fails.

Upon service booking, a copy of the confirmed service form will be forwarded to both the end user as well as the corresponding PI.

Initial sample submission evaluation (sample quality, amount, etc) is recommended to optimize sample quality, depending on the sample nature. Potential experimental discussion(s) might be arranged prior to samples submission.

The complete workflow take approximately 2 full working days. As only limited amount of samples can be performed per week, users are encouraged to optimize their sample quality before submission. Service bookings are arranged on a first-come-first-serve basis.

Once the service has started, service charge would be accounted for FULL service package price, as the reagents are on package stock basis. We are pledged to provide our service in a reasonable, efficient manner with quality.

Useful Resources

10X Genomics – Single Cell Gene Expression

10X University – A step-by-step learning and training environment

10X Datasets

10X Publications

Worthington Tissue Dissociation Guide


Dr Joaquim Vong  
Scientific Officer  
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
Tel no: 39430318
Ms. Chloe Chen  
Research Assistant  
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
Tel no: 39435240
Location: LIBSB Room 525
Lab no.: 39434373