Illumina Workflow Full Service


We offer a Full Service option for the standard applications listed below using validated library prep methods. We have an average turnaround time of about 4 weeks after the samples pass QC. If your sample doesn't reach the sample requirements of our standard protocols, we can suggest other protocols and we can continue with the experiment via our custom service mode or user lab mode.
You can find how to access our User Lab HERE

Standard Service Offerings, Applications and Sample Requirements:


Applications Protocols Offered Optimum Input Requirements Standard Sequencing Recommendations
1. mRNA Sequencing Illumina TruSeq mRNA Stranded 600 ng - 1 μg Total RNA, DNAse treated, column purified 20M reads, single read 100 bp
2. Total RNA Sequencing Illumina TruSeq TotalRNA Stranded (HMR) 600 ng - 1 μg Total RNA, DNAse treated, column purified 40M reads, single read 100 bp
3. Low Input RNA Sequencing Clontech Picomammalian, SmartSeq2 less than 10 ng Total RNA 20-40M reads, single read 100 bp
4. Small RNA Sequencing RealSeq 1 ng - 1 μg Total RNA, DNAse treated 10M reads, single read 75 bp
5. Single cell RNA Sequencing Droplet Based 10X Genomics Single Cell 1’000 - 10’000 viable cells in a tube.50’000 reads per cell
6. Single cell RNA Sequencing Plate Based Smartseq2 384 well plate Single Cell Cells sorted in 384 well plates1M reads per cell
7. Whole Genome Sequencing TruSeq DNA Nano, TruSeq PCR Free, NEB Ultra II 600 ng - 1'000 ng high MW genomic DNA 30X coverage, paired end 150 bp
8. Low Input Whole Genome Sequencing NEB Ultra II, Nextera XT 1 - 10 ng high MW genomic DNA 30X coverage, paired end 150 bp
9. Whole Small Genome Sequencing Nextera XT 1 - 10 ng genomic DNA paired end 150 bp
10. Metagenomics Amplicon Barcoding inquire inquire
11. Chip Seq NEB Ultra 10 ng Single ChIP enriched DNA or input DNA 20M reads per sample, single read 100 bp
12. Ready-Made Libraries 10 nM, pooled custom
13. Spatial Transcriptomics 10X Visium FFPE custom


Please click on the application or protocol of your choice for a more detailed information (ie sample requirements, experimental design considerations).
Illumina Sequencing Pricing
How to submit samples for Illumina/Short Read Sequencing.pdf
How to submit Ready-made Libraries.pdf


Sequencing instrumentation



SequencersIlumina NovaSeq Ilumina NextSeq 2000 llumina NextSeq 500 Ilumina MiSeq Ilumina MiniSeqIlumina iSeq
Image Image Image Image Image Image
Flowcell SP, S1,S2,S4 P2, P3 High Output, Mid output High Output, Mid output High Output, Mid output
Key FeaturesPatterned Flowcell Patterned Flowcell Non-Patterned Flowcell Non-Patterned Flowcell Non-Patterned Flowcell Nanowells, CMOS
Reads (SE) per FC S4 8 Billion P3 1.1B HO 350 Million 25 Million HO 22 Million 4Million
SP 650-800M P2 400M MO120 Million MO 7 Million
Max Read Length 2X150 bp, SP 2X250 2X150 bp 2X150 bp 2X300 bp 2X150 bp 2X150 bp
Approx Price per Gb S4-12.10 chf, S1-25.9 chf 46.5 chf 196.8 chf 282 chf 925 chf
Key Applications Large WGS, RNA Seq Single cell SequencingATAC Seq, ChIP Small WGS, Amplicons Small WGS, QCs Small WGS
Single Cell small RNA Targeted Sequencing, QCs
Access Mode Service Walk-in Service, Walk-in Service, Walk-in Service, Walk-in Service, Walk-in
Location Irchel Campus GEML Honggerberg Irchel Campus Irchel Campus Irchel Campus Irchel Campus
Irchel Campus GEML Honggerberg

Images are from https://www.illumina.com
Illumina Sequencing Pricing
How to submit samples for Illumina/Short Read Sequencing.pdf
How to submit Ready-made Libraries.pdf

Sample Submission Guidelines


STEP 1 : Project Registration.

Please register for a project in B-Fabric. All services in NGS require a project submission via B-​Fabric, our project management system. Register for a project here.
As a project applicant/manager, you can add members to your project. These members can make orders and access project data. For more information about the data access rights, please click here.

STEP 2 : Assigning a Project Coach

You will be assigned a project coach, who will be your main FGCZ contact. Your project coach will invite you for a meeting to discuss your project in-depth together with one of our bioinformaticians.
This step is where you will settle on the best experimental design, library prep approach, sequencer and data analysis method for your research question. Your coach will review the project and forward it for approval.

STEP 3 : Create an order and sample registration

Once your project is approved, you may create an order and register the samples.
Instructions to fill out the form is here
How to submit samples for Illumina/Short Read Sequencing.pdf
How to submit Ready-made Libraries.pdf

STEP 4 : Offer Generation and Order Acceptance

Will will check the order and then make an offer. This step is where the FGCZ will commit to the deliverables and allow the you to check for the total cost of the experiment.

STEP 5 : Sample drop-off

If you agree to the terms in Step 4, you may bring your samples.
Do not bring or send samples which are not properly labeled with Bfabric IDs.
You can either bring the samples by hand or send them via post/courier.
We are glad to accept your samples between 9am to 5pm.
Our address: Functional Genomics Center Zurich, Sequencing Platform, Y59G90, Winterthurerstr. 190, 8057 Zurich SWITZERLAND
Please specify the name of your coach.

STEP 6 : Sample Tracking

You will receive an automated email (gfeeder) every time we reach a milestone in the sample preparation.

STEP 7: Data Delivery

Your data will be delivered via Bfabric.

STEP 8: Data Analysis

If you opted for bioinformatics analysis, our bioinformaticians will contact you about data analysis.

STEP 9: Invoicing

Full Service Workflow Process and Turnaround Times


Our normal turnaround time is 4-6 weeks. Once we receive samples, we proceed directly with the processing of your samples. We receive double to triple the number of samples around June-August and November-December. This results in a slight increase in our turnaround time during these periods.

This illustration summarizes our workflow.

Image


Data Access Policy


Project data can be accessed by active members of the project. Project managers can remove or give access rights in the B-Fabric project page.

Still have some questions? Please email sequencing@fgcz.ethz.ch

Resources

Coverage Calculator
FGCZ apps
RNA Quality Explained
Library QC Explained
How to submit samples for Illumina/Short Read Sequencing.pdf
How to submit Ready-made Libraries.pdf
Acknowledgements and Authorships
Introduction Slides


Back to FGCZ Main Page