Service Charges and Ordering
The Core offers comprehensive NGS services including nucleic acid extraction, library preparation, NovaSeq/MiSeq sequencing and Bioinformatics services.
Please contact Dr KWOK, Hin ( firstname.lastname@example.org / 2831-5483) or platform specialists for project discussion and official service quotation.
Price vary with the following factors:
- Throughput or fold coverage required (sequencing reads or bases output)
- Read type and length (Single Read or Paired-end Read, 50 bp to 300 bp)
- Type of work (DNA shotgun sequencing, RNA-seq, small RNA-seq, ChIP-seq, metagenomics etc.)
- Number of samples
- GC content of samples
- Method for library preparation
- Bioinformatics analysis needs
- Special and/or additional requirements
- Affiliated institute (HKU, local academics, oversea academics and commercial company)
Please refer to Sample Requirement and Submission page for sample requirements.
Please submit service request through iLab.
Different library preparation options are available.
Depending on application, the Core may provide up to 384-index combination# for library construction and sequencing.
We will be happy to discuss your needs and provide recommendations.
#Unique Dual indices with Unique Molecular Identifier (UMI) are available. Please enquire.
NovaSeq 6000 Specifications (from illumina):
MiSeq Specifications (from Illumina):
^The Core routinely runs NovaSeq with 2 x 150bp read length. For other read length, please enquire.
*Install specifications based on Illumina PhiX control library at supported cluster densities. Performance may vary based on sample quality, nucleotide diversity , cluster density, and other experimental factors. Illumina cannot guarantee the Q30 and quality for low diversity library even with PhiX spiked in.
Sample Requirement and Submission
Full Service [Library preparation + Sequencing Run]
A. Sample Preparation
Pure DNA and RNA are crucial to ensure consistent library preparation and quality data.
- Use column purification
- Apply column re-purification for samples purified with phenol/chloroform methodology
- Treat DNA with RNase
- Treat RNA with DNase
Generally, samples should be:
- Free of inhibitors, e.g. heme (from blood), EDTA and salts
- Free of organic solvents, e.g. phenol, chloroform and ethanol
- Free of cellular debris or proteins
- Dissolved in buffer at proper pH, e.g. 10mM Tris-HCl at pH 8.5
- Not degraded, i.e. high-molecular weight, double-stranded genomic DNA and RNA with high RIN score on bioanalyzer
- Free of EDTA especially if Nextera library preparation is to be used, i.e do NOT dissolve in Tris-EDTA (TE) buffer
Before sample preparation, please contact platform specialists to confirm sample submission logistics.
B. Sample Requirements
Both DNA and RNA shall be assessed by UV spectrophotometry for purity and quantity estimation before sample submission. Gel photos are also required for some of the DNA-based applications.
After sample submission, sample QC will be performed by the Core platform specialists, which includes
- Qubit quantification for both DNA and RNA samples
- Bioanalyzer RNA quality assessment for RNA samples (at cost)
Refer to below table for sample submission requirement of each application, please submit sample with minimum volume of 10 μL in a clearly labeled 1.5 mL low-retention microcentrifuge tube.
* We request more than protocol input amount because of 2 reasons:
(1) we need extra for sample QC before library construction.
(2) we note that most users quantify samples with O.D. measurement, e.g. Nanodrop, which in most cases over-estimate DNA/RNA quantity.
We will keep samples properly and return any leftover.
If your samples do not meet above requirements, please contact us and we can seek alternatives together.
C. Sample Submission
To request a service, please utilize iLab and ensure to upload the completed sample submission form that corresponds to the application. As CPOS is in the process of implementing Agilent SLIMS for SS100 and SS300 projects, the forms for both services are tailor made.
- For SS100 service (DNA-Seq project): Sample-Submission-Form-SS100 (and attach the DNA gel photo with appropriate size marker to the iLab job)
- For SS300 service (RNA-Seq project): Sample-Submission-Form-SS300
- For other NGS services : Sample-Submission-Form
Please contact our colleagues in advance (via phone/email) prior to your on-site sample submission.
We accept a single tube of pre-made library for sequencing run service.
Indexed library pooling (if required) should be completed and the index information shall be sent to the Core before library submission.
Library QC (bioanalyzer for size and qPCR for quantity) is included for ONE library (or a SINGLE pool of libraries) per batch of sequencing.
Here is the guidelines using BLAST search to check the index sequence orientation.
General submission requirements for each tube of pre-made library:
- Not less than 10 ng/uL or 20nM
- Minimum volume of 20 uL
- optimal library size of 300 – 700 bp
Submit pre-made library with:
- Hardcopy (and softcopy as attachment in iLab) of the Library Submission Form
Attach the information in iLab:
- Library Submission Form (soft copy in excel format)
- Official library preparation protocol
- Index i7 and i5 sequences
- Index i7 and i5 sequences with full adapter sequences (if customized protocol or custom ordered adapter oligo used)
Please consult platform specialists before submission.
Once data is available, users will be notified via email. Details of data colocation, please refer to CPOS Bioinformatic Core page.
Terms of Service
Please refer to Technical Details for the information.
The actual throughput, however, will vary with the following factors:
- Cluster Density
- CG content of the samples
- Reagent lots
- Other run-to-run variations
Data Quality and Availability
We will in good faith produce the best output and quality data to all collaborators and users.
Any issues will be discussed openly before, during and after the run.
Data at various steps are also available to share with collaborators and users upon request.
Turnaround Time is valid for project size <= 80 samples. Please contract us for service TAT info if project size >80 samples.
Turnaround Time is valid while stock reagent available, else additional several weeks for reagent ordering and delivering will be needed.
CPOS is willing to help researchers on R&D projects and urgent needs, please don’t hesitate to discuss with us about your plan.
* Adapter Trimming will NOT be selected by default for MiSeq Sequencing run service. If you need Adapter Trimming, please specify prior to project confirmation.
Dr KWOK, Hin
Ms KONG, Carol