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 plates	1M 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

Sequencers	Ilumina NovaSeq	Ilumina NextSeq 2000	llumina NextSeq 500	Ilumina MiSeq	Ilumina MiniSeq	Ilumina iSeq
Flowcell	SP, S1,S2,S4	P2, P3	High Output, Mid output	High Output, Mid output	High Output, Mid output
Key Features	Patterned 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 Sequencing	ATAC 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.

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