FGCZ Genomics > Services
We offer full package services including project discussion, DNA/RNA quality Control, Library Preparation, Sequencing and data QC. Downstream Data Analysis is provided upon request.
Experienced users can also bring their ready made libraries and pay only for the Sequencing part. The protocols we do not offer in service mode could be done in user lab mode.
Jump to
PacBio Sequencing |Oxford Nanopore Sequencing
The PacBio sequencing uses the SMRT (Single Molecule Real Time) technology, which enables the real-time detection of nucleotide incorporation events during the elongation of the replicated strand from the non-amplified template. SMRT sequencing supports numerous sequencing applications including targeted or whole genome sequencing, RNA isoforms and epigenetic modifications.
The PacBio av. Read length and output refer to the Polymerase read length.
The final output and the Polymerase read length may vary from sample to sample.
The DNA sample must be possibly delivered in a low salt buffer like the Qiagen Elution Buffer (10mM Tris-Cl, pH 8.5-9.0)
Please use a Qubit system or picogreen method in order to quantify your samples.
Spectrophotometric quantitation tends to over estimate the concentration.
1 Library should be enough to sequence from 1-4 Sequel SMRT cells, depending on the recovery yield.
DNA Extraction and Quality Control
Nanopore sequencing enables direct, real-time analysis of long DNA or RNA fragments. It works by monitoring changes to an electrical current as nucleic acids are passed through a protein nanopore. The resulting signal is decoded to provide the specific DNA or RNA sequence.
Our turn around times are from 4 to 6 weeks, upon sample submission.
Users that require very fast processing times are welcome to prepare the libraries and bring them to the FGCZ for sequencing.
The GridIONX5 and the P2 Solo are also accessible in walk in mode, for trained users.
Protocols available as full service: sample QC, library prep, sequencing, raw data delivery and data analysis (optional).
- DNA Sequencing by ligation, with or without native barcoding
Protocols supported in user lab mode: bring your kits and you do the library yourself, under our supervision
- rapid DNA sequencing
- 16s metagenomics
- direct cDNA or PCR-cDNA Sequencing
- direct mRNA Sequencing
- any other protocol you would like to try
The av. Read Length depends on the size of the DNA library
cDNA PCR kit= 200 ng of total RNA per flow cell to be sequenced
direct cDNA kit= at least 100 ng Poly(A)+ RNA or 1 µg of total RNA per flow cell to be sequenced
- is double-stranded; single-stranded DNA is not compatible with the library preparation process.
- has not undergone multiple freeze-thaw cycles as they can lead to DNA damage.
- has not been exposed to high temperatures (e.g.: > 65oC for 1 hour can cause a detectable decrease in sequence
quality), pH extremes (< 6 or > 9).
- has an OD260/OD280 ratio of 1.8 to 2.0.
- does not contain insoluble material.
- does not contain RNA contamination.
To maximize read length and quality, it is essential that your DNA sample:
- is double-stranded; single-stranded DNA is not compatible with the library preparation process.
- has not undergone multiple freeze-thaw cycles as they can lead to DNA damage.
- has not been exposed to high temperatures (e.g.: > 65oC for 1 hour can cause a detectable decrease in sequence
quality), pH extremes (< 6 or > 9).
- has an OD260/OD280 ratio of 1.8 to 2.0.
- has an OD260/OD230 ratio of 1.8 to 2.3.
- does not contain insoluble material.
- does not contain RNA contamination.
- has not been exposed to intercalating fluorescent dyes or ultraviolet radiation. SYBR dyes are not DNA
damaging, but do avoid ethidium bromide.
- does not contain denaturants (e.g., guanidinium salts or phenol) or detergents (e.g., SDS or Triton-X100).
- does not contain carryover contamination from the original organism/tissue (e.g., heme, humic acid,
polyphenols, etc.)
a. Avoid incubation in complex or rich media.
b. Harvesting from several cultures rather than a single, high-density culture during early- to mid-
logarithmic growth phase is preferred.
c. Extraction of small volumes is preferred over large volumes to avoid accumulating high concentrations
of potentially inhibiting secondary components.
Questions? Please email sequencing at fgcz.ethz.ch.
phone: 063 44 6353911 (For pressing issues only please. We prefer if you email us because we are mostly working in the lab so we can't always attend to phone calls)
FGCZ Genomics > Services
Long Read Sequencing Services
We offer full package services including project discussion, DNA/RNA quality Control, Library Preparation, Sequencing and data QC. Downstream Data Analysis is provided upon request.
Experienced users can also bring their ready made libraries and pay only for the Sequencing part. The protocols we do not offer in service mode could be done in user lab mode.
Jump to
PacBio Sequencing |Oxford Nanopore Sequencing
PacBio Sequencing
The PacBio sequencing uses the SMRT (Single Molecule Real Time) technology, which enables the real-time detection of nucleotide incorporation events during the elongation of the replicated strand from the non-amplified template. SMRT sequencing supports numerous sequencing applications including targeted or whole genome sequencing, RNA isoforms and epigenetic modifications.
Instruments & Specs:
| Sequel IIe | Revio | |||
| 
| |||
| SMRT Cell Type | 8M Cell | 25M Cell | ||
| Pol. read Number | 4-6 M | 12-18M | ||
| gDNA library | ||||
| av. Pol. read length HiFi mode | 70+ Kb | 70+ Kb | ||
| expected output HiFi mode | 20+ Gb | 60-100Gb | ||
| Amplicons/Iso-Seq library | ||||
| av. Pol. read length | 20+ Kb | 14-17 Kb | ||
| number HiFi Reads | 1.5-2.5 M | 7.5M | ||
| Location | in house | outsourced | ||
The PacBio av. Read length and output refer to the Polymerase read length.
The final output and the Polymerase read length may vary from sample to sample.
Services and Prices
Input Material needed for library prep
| Library Protocol and Insert size | Input | |||
| Amplicons <3 Kb | 300ng | |||
| Amplicons 3-10 Kb | 500ng | |||
| Amplicons >10 Kb | >1000ng | |||
| 16S rRNA amplicon pool | 1000ng | |||
| gDNA Standard HiFi 15-18 Kb | 3-5µg | |||
| gDNA Low Input HiFi 15 Kb | >400n | |||
| gDNA Microbial Multiplexing HiFi 7-10 Kb | 300-1000ng | |||
| gDNA Shotgun Metagenomics HiFi 10 Kb | >300ng | |||
| Iso-Seq | 300ng total RNA | |||
The DNA sample must be possibly delivered in a low salt buffer like the Qiagen Elution Buffer (10mM Tris-Cl, pH 8.5-9.0)
Please use a Qubit system or picogreen method in order to quantify your samples.
Spectrophotometric quantitation tends to over estimate the concentration.
1 Library should be enough to sequence from 1-4 Sequel SMRT cells, depending on the recovery yield.
PacBio Recommended DNA extraction methods
Best practices sheets for key PacBio APPLICATIONS
Multiplexing
Protocols and recommendations for multiplexingImportant measures impacting DNA quality
For most applications it is crucial that the extracted gDNA is of HMW (High-molecular-weight) and does not contain any impurities (see below). Please have a look at the following technical note from PacBio first:DNA Extraction and Quality Control
Oxford Nanopore Sequencing
Nanopore sequencing enables direct, real-time analysis of long DNA or RNA fragments. It works by monitoring changes to an electrical current as nucleic acids are passed through a protein nanopore. The resulting signal is decoded to provide the specific DNA or RNA sequence.
Protocols and support modes
Our turn around times are from 4 to 6 weeks, upon sample submission.
Users that require very fast processing times are welcome to prepare the libraries and bring them to the FGCZ for sequencing.
The GridIONX5 and the P2 Solo are also accessible in walk in mode, for trained users.
Protocols available as full service: sample QC, library prep, sequencing, raw data delivery and data analysis (optional).
- DNA Sequencing by ligation, with or without native barcoding
Protocols supported in user lab mode: bring your kits and you do the library yourself, under our supervision
- rapid DNA sequencing
- 16s metagenomics
- direct cDNA or PCR-cDNA Sequencing
- direct mRNA Sequencing
- any other protocol you would like to try
Instruments & Specs
| Flongle | GridION X5 | P2 Solo | Promethion 24 | |
| Flow Cell Type | Flongle R9.4.1, R10.4.1 | MinION R9.4.1, R10.4.1 | PromethION R9.4.1, R10.4.1 | PromethION R9.4.1, R10.4.1 |
| gDNA | ||||
| av. read length | 10-30 Kb | 10-30 Kb | 10-30 Kb | 10-30 Kb |
| expected output | up to 1Gb | 4-15 Gb | 30-90 Gb | 30-90 Gb |
| cDNA/ amplicons | ||||
| av. read length | 1-10 Kb | 1-10 Kb | 1-10 Kb | 1-10 Kb |
| number of reads | 0.2-0.5M | 1-10 M | 40-70M | 40-70M |
| direct RNA | ||||
| av. read length | N/A | 1-2kb | 1-2kb | 1-2kb |
| number of reads per FC | N/A | up to 1M | up to 3M | up to 3M |
The av. Read Length depends on the size of the DNA library
Services and Prices
Recommended input amounts
DNA Ligation kit= at least 2ug of gDNA for each flow cell to be sequencedcDNA PCR kit= 200 ng of total RNA per flow cell to be sequenced
direct cDNA kit= at least 100 ng Poly(A)+ RNA or 1 µg of total RNA per flow cell to be sequenced
Important measures impacting DNA quality
To maximise read length and quality, it is essential that your DNA sample:- is double-stranded; single-stranded DNA is not compatible with the library preparation process.
- has not undergone multiple freeze-thaw cycles as they can lead to DNA damage.
- has not been exposed to high temperatures (e.g.: > 65oC for 1 hour can cause a detectable decrease in sequence
quality), pH extremes (< 6 or > 9).
- has an OD260/OD280 ratio of 1.8 to 2.0.
- does not contain insoluble material.
- does not contain RNA contamination.
To maximize read length and quality, it is essential that your DNA sample:
- is double-stranded; single-stranded DNA is not compatible with the library preparation process.
- has not undergone multiple freeze-thaw cycles as they can lead to DNA damage.
- has not been exposed to high temperatures (e.g.: > 65oC for 1 hour can cause a detectable decrease in sequence
quality), pH extremes (< 6 or > 9).
- has an OD260/OD280 ratio of 1.8 to 2.0.
- has an OD260/OD230 ratio of 1.8 to 2.3.
- does not contain insoluble material.
- does not contain RNA contamination.
- has not been exposed to intercalating fluorescent dyes or ultraviolet radiation. SYBR dyes are not DNA
damaging, but do avoid ethidium bromide.
- does not contain denaturants (e.g., guanidinium salts or phenol) or detergents (e.g., SDS or Triton-X100).
- does not contain carryover contamination from the original organism/tissue (e.g., heme, humic acid,
polyphenols, etc.)
These are general recommendations to help maintain high molecular weight DNA.
Before DNA extraction:a. Avoid incubation in complex or rich media.
b. Harvesting from several cultures rather than a single, high-density culture during early- to mid-
logarithmic growth phase is preferred.
c. Extraction of small volumes is preferred over large volumes to avoid accumulating high concentrations
of potentially inhibiting secondary components.
Questions? Please email sequencing at fgcz.ethz.ch.
phone: 063 44 6353911 (For pressing issues only please. We prefer if you email us because we are mostly working in the lab so we can't always attend to phone calls)
FGCZ Genomics > Services