Service Charges and Ordering
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.
Technical Details
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.
Workflow
Sample Preparation and Submission
Cell requirement for 3′ or 5′ gene expression studies
For each sample, users are asked to submit a cell suspension of
– concentration 500 – 1000 cells per μl
– size 30 μm or smaller
– well-dissociated without clumps or doublets
– good viability (>85% viable)
– re-suspended in 1x PBS + 0.04% BSA (or other buffer recommended by vendor)
Please refer to vendor’s protocol on sample preparation.
Sample Submission
Please contact our colleagues in advance (via phone/email shown here) before bringing the samples to the Core.
After sample submission date and details confirmed, please submit service request through iLab.
Please submit Single Cell (10X Genomics) sample submission form as attachment in iLab.
Useful Links
Contact
Dr KWOK, Hin
Ms LUI, Schwan