Steven Kembel, PhD
Catherine Laprise, PhD
Geneviève Bourret, MSc
Preparation of samples
Agilent 2100 Bioanalyzer
- Measures fragment size from 50-7000bp with an accuracy of ± 10%
- Quantifies from 0.5-500pg /µl with an accuracy of 20%
- Quantification of DNA and RNA in the same sample
- DNA quantification: 10pg/µL – 1µg/µL
- Volume required: 1µL
- Quantification of DNA, RNA, and Proteins
- DNA quantification: 2ng /μl – 27.5μg /μl
- Detection of contaminants (phenol, proteins)
- Volume required: 1µL
Preparation of amplicon libraries (16S, ITS, etc ...)
The Amplicon Library Preparation Service includes PCR, library preparation and Miseq sequencing (V3 kit, 600 cycles). Amplicon will be multiplexed (up to 384 samples per Miseq, including positive and negative controls). You will get a reading of approximately 30,000 reads /sample. If you require a higher sequencing depth (fewer samples per Miseq) please contact us before submitting your samples, additional charges may apply.
It is also possible to use the library preparation service without sequencing. In this case, please contact us.
The platform provides the primers for 16S and ITS amplification (see below for available primer pairs). These primers contain the Illumina adapters needed for sequencing, the indexes that allow multiplexing of the samples, and the specific amplification sequence. It is also possible to order custom primers (additional charges apply) if they are not on the list.
List of primers:
- Forward primer 799F (séquence 5’->3’) : AACMGGATTAGATACCCKG
- Reverse primer 1115R (séquence 5’->3’) : AGGGTTGCGCTCGTTG
- Forward primer 515F (séquence 5’->3’) : GTGYCAGCMGCCGCGGTAA (Parada et al. 2015)*
- Reverse primer 926R (séquence 5’->3’) : CCGYCAATTYMTTTRAGTTT
*V4-V5 primers also amplify 18S. This primer pair is therefore not recommended for samples containing substantial contamination with host DNA (Parada et al. 2015).
- Forward primer ITS1F (séquence 5’->3’) : CTTGGTCATTTAGAGGAAGTAA
- Reverse primer ITS2 (séquence 5’->3’) : GCTGCGTTCTTCATCGATGC
Custom primers can be ordered to suit your needs (additional charges apply).
CERMO-FC members and UQAM researchers are invited to contact us to find out about privileged pricing thanks to the support of CERMO-FC.
PCR and Miseq v3 sequencing, 600 cycles*
- <376 samples: $20 /sample
- >376 samples: $18 /sample
*Additional charges apply for custom primers. Consult the amplicon library preparation section to know the primer sequences provided by the platform.
PCR and Miseq v3 sequencing, 600 cycles *
- <376 samples: $25 /sample
- >376 samples: $23 /sample
* Additional charges apply for custom primers. Consult the amplicon library preparation section to know the primer sequences provided by the platform.
An administrative charge of 15% may be applicable.
Others types of libraries
Shotgun DNA Libraries
Up to 96 indexes available. Flexible starting amount of DNA. The DNA provided must be of good quality (with no residual traces of protein, salts or other contaminants) and eluted in water or an EDTA-free buffer.
Shotgun-type DNA libraries with or without PCR can be made, using the QIAseq FX DNA kit from Qiagen. The libraries produced are compatible with any Illumina sequencer.
- up to 96 indexes available
- flexible starting amount of DNA
- the DNA provided must be of good quality (with no residual traces of protein, salts or other contaminants) and eluted in water or an EDTA-free buffer.
It is possible to offer you an RNA library preparation service, with the upstream possibility of enriching the mRNAs or depleting the rRNAs. These libraries are compatible with any Illumina sequencer.
For profiling studies we can produce 3 ’mRNA seq libraries which require fewer reads / sample than a regular RNA-seq.
For any project with RNA, please contact the platform before submitting your samples.
The genomics platform offers a service for genotyping your animals.
The genotyping service includes extracting DNA (HotSHOT method) from a mouse ear punch, PCR reaction, and producing a results report.
Do you want to genotype other types of animals? Please contact us.
Mouse genotyping results are usually delivered within 48-72 hours of receipt of samples.
Do you have a specific deadline to meet? Please contact us.
I am very happy with the level of technical support and the quality of data produced by the CERMO-FC genomics platform. Genevieve was very generous with her advice she gave to the students regarding the preparation of their samples, quality control in terms of techniques, and estimated costs for their projects.
Publications resulting from samples analysis by the CERMO-FC platform
FAQ - Frequently Ask Questions
You can bring your samples in person at the address below. It is recommended to announce your visit in advance to ensure the presence of someone to receive your samples.
** Not available until further notice due to the COVID19 pandemic
Plateforme de génomique CERMO-FC
Pavillon des sciences biologiques UQAM SB-2130
141 avenue du Président-Kennedy
You can also have your samples delivered by a carrier to the address below. The transport of samples is at the expense of the applicant. The CERMO-FC genomics platform is not responsible for damage or loss of samples during transport.
Plateforme de génomique CERMO-FC
Quai de réception PK, UQAM SB-2130
2005 rue Jeanne-Mance
Yes. The platform is continually working on developing new protocols and new services to offer. Please do not hesitate to contact us to discuss your genomics project even if it is not on the list of services offered.
-It is recommended to send only an aliquot of the samples.
-To avoid evaporation and cross-contamination between samples during transport, be sure that all tubes and / or plates are properly sealed
– All tubes and / or plates should be clearly identified. Do not forget to attach the associated sample submission.
-RNA and DNA samples as well as tissues should be sent on dry ice.
If you have any doubt, please contact us before sending your samples.
Received samples will go under a quality control test. If any problems, the user will be contacted.
Yes. After receiving the samples, a quality control is carried out. Non-compliance of samples may cause delay and/or additional costs (e.g. optimization of protocols, quantification of samples, purification of samples, etc.). The user will be contacted in the event of a problem.
Reading length refers to the number of base pairs (bp) sequenced from a DNA fragment. The Miseq allows up to 2 x 300 bp in paired-end read or 600 cycles of sequencing.
Genome sequencing requires for each base a unique sequencing. However for most applications, to have an accurate base assignment process, each base needs to be sequenced several times. Next-generation sequencing (NGS) coverage describes the average number of reads that align to, or “cover,” known reference bases
Before you begin an experiment involving next-generation sequencing, you need to know the depth of sequencing you want to achieve. Most users determine the necessary coverage level based on the type of study, gene expression level, size of reference genome, published literature and best practices defined by the scientific community.
Illumina does not have an official recommendation for the level of sequencing coverage, but this technical note can help you estimating that coverage: Estimating Sequencing Coverage
This estimator helps with determining the reagents and sequencing runs that are needed to arrive at the desired coverage for your experiment: calculate sequencing coverage
The sequencing data obtained after MiSeq sequencing will be demultiplexed and delivered in FASTQ format. For single-read (SR) sequencing, only one FATSQ file will be created per sample (R1). For a paired-end (PE) analysis, two FASTQ files will be created per sample (R1 and R2). For more information on FASTQ files see the following Illumina bulletin: FASTQ files explained
The genotyping service includes the extraction of DNA from a mouse ear punch, a PCR reaction and a results report.