Single Cell (10X Genomics)

Single Cell 3′ Gene Expression Analysis

• 3′-end gene expression profiling of 500 – 10,000 cells per sample

Single Cell 5′ Gene Expression & Immune Profiling

• 5′-end gene expression profiling of 500 – 10,000 cells per sample
• Assemble, annotate full length T cell and/or B cell V(D)J sequences and call clonotypes
• Able to examine gene expression profile and resolve TCR/BCR repertoires from the same sample

Single Cell ATAC Sequencing

• Assess chromatin accessibility on single cell level
• Work on nuclei isolated from single cells
• Profiling 500 to 10,000 nuclei per sample

Self-service (please enquire)

• For non-working hours usage (after 17:30 on weekdays, whole days on weekends)

Service prices

Range from approximately HK$ 16,000 to HK$ 30,000 per sample, varies with the following factors:

• Number of samples per submission
• Applications (e.g. 3′ gene expression, 5′ gene expression, V(D)J analysis, etc)
• Number of target cells (affecting the sequencing cost)
• Needs in bioinformatics analysis
• Affiliated institute (HKU, local academics, overseas academics, etc)

**The price covers cell encapsulation to library preparation
**Sequencing cost NOT included

The Core offers 10X Chromium Single Cell Controller run to encapsulate single cells from cell suspension, subsequent library preparation and Illumina sequencing.   Please contact Dr KWOK, Hin (singlecell10x.cpos@hku.hk / 2831-5483) for project discussion.

Service ordering

Please refer to Sample Preparation and Submission section for sample requirements.

Please submit service request through iLab.

Single cell encapsulation

The system is able to capture 500 to 10,000 cells per sample from a single cell suspension.
Users are required to submit a cell suspension of 500 – 1000 cells per μl, of size 30 μm or smaller and of good viability (85% or above).
Cells will be encapsulated into Gel Beads-in-emulsion (GEMs) by the 10X Chromium Single Cell Controller, followed by reverse transcription and library preparation to become a pool of cDNA libraries.
Transcripts from the same cell will be identified by a barcode, while each of these transcripts will be discernable from one another by a Unique Molecular Identifier (UMI).

Source: 10X Genomics

Library Preparation

The service will include library preparation after single cell encapsulation.

Sequencing Run

Libraries generated are compatible with Illumina sequencers. In order to read the transcript sequences on one end, and the barcode and UMI on the other end, paired-end sequencing reads are required.
Vendor’s specification recommends getting at least 20,000 paired-end raw reads per cell for gene expression studies*.

* Reads per cell required is very cell-type dependent, it is recommended to obtain more reads per cells at the optimization stage.