GENOM'IC performs RNA and DNA quality control on two Agilent Bioanalyzer 2100 for any type of team in the form of 4 services. These quality controls will allow for example to validate the quality of total RNA, small RNA or immunoprecipitated DNA profiles.

In practice:

The client provides an aliquot of his samples accompanied by the QCBioA submission form (forms section). In return, the core facility sends him the report of the run by email. Four paid services are available:

• Bioanalyzer Nano (total RNA concentrations between 5 and 500 ng/µL)
• Bioanalyzer Pico (total RNA concentrations between 50 pg and 5 ng/µL)
• Bioanalyzer Small (total RNA concentration between 1 and 100 ng/µL; enriched small RNA concentration between 1 and 20 ng/µL)
• Bioanalyzer HS (DNA concentrations between 5 and 500 pg/µL)

The user provides us with at least 3 µL of sample in 0.2 mL or 0.5 mL RNAse and DNAse free microtubes accompanied by the completed Bioanalyzer submission form and the report of measurements of the concentrations of the samples obtained on a Nanodrop.

Nanodrop 1000 and 2000 are made available to the teams in each building of the Institute. These devices are placed under the responsibility of the buildings.

The facility offers transcriptome analysis services based on Affymetrix technology. It has a GCS3000 7G station with three fluidic stations and three hybridization ovens. The basic service includes all the steps from the processing of RNA samples provided by the customer to the statistical analysis of the data to obtain a list of differentially expressed genes.

A solution for the functional analysis of data can be proposed (training in the use of IPA and provision of dedicated analysis stations). You can contact Morgane LeGall for more information.

The facility offers all types of Affymetrix expression chips (especially the latest generations of Gene2.0ST, Clariom and XTA chips) and adapts its protocols to the quality and quantity of material provided by the customer:

• for RNAs with an RIN > 7, we will use standard chemistry (called standard WT) for amounts of total RNA between 50 and 500 ng.

Another chemistry (called Pico) will be used for amounts of total RNA between 200 pg and 50 ng.

• for RNA extracted from FFPE cuts, we will use standard chemistry (called WT pico) for amounts of total RNA between 0.2 and 10 ng.

Another chemistry (called NuGen One) will be used for single cell analysis projects.

In practice:

• for regular users, complete and send the Puce Project submission form  by e-mail.
• otherwise, contact us either by e-mail or on 01 40 51 65 65.

The core facility offers transcriptome sequencing services (total, coding, small RNA) or RNA-Seq based on the use of Illumina NextSeq 500.

From the RNA provided by the customer, the basic service includes the quality control of the samples, the production of the libraries, their sequencing and the quality control of the raw data. The sequencing approaches (single or paired readings, depth of readings) are flexible and adaptable according to the project. Each project will be the subject of an adapted estimate taking into account these different aspects.

GENOM'IC also offers an analysis service of the reads produced (alignment and quality control of the alignments) and a statistical analysis of these data making it possible to obtain a list of differentially expressed genes.

The various RNA-Seq services offered include quality control of RNA provided by the customer, preparation and sequencing of the library and quality control of the data produced.

We distinguish :

- Sequencing of the coding transcriptome after polyA selection

• Principle: selection of messenger RNAs with oligo dT beads, then Reverse Transcription in cDNA (conservation of the meaning of the transcripts), ligation of Illumina adapters and amplification by PCR.
• Amount of total RNA: 100 ng – 4 µg
• Recommended RNA quality: RIN > 8
• Kit Used: TruSeq mRNA Stranded (Illumina)
• Sequencer: NextSeq 500 (2 x 75bp and 1 x 75bp)

- Sequencing of the total transcriptome by ribosomal depletion

• Principle: depletion of ribosomal RNAs (cytoplasm + mitochondria) with biotinylated probes (on beads), then Reverse Transcription in cDNA (conservation of the meaning of the transcripts), ligation of Illumina adapters and amplification by PCR.
• Amount of total RNA: 500 ng – 4 µg
• Recommended RNA quality: RIN > 8
• Kit Used: TruSeq Total RNA Stranded (Illumina)
• Sequencer: NextSeq 500 (2 x 75 bp and 1 x 75 bp)

- Small RNA sequencing

• Principle: from purified small RNA or total RNA, oriented adapter ligation, RT-PCR and gel purification.
• Amount of total RNA: 1 µg
• Amount of purified small RNAs: 10-50 ng
• Kit used: TruSeq Small RNA Library Prep Kit (Illumina)
• Sequencer: NextSeq 500 (1 x 75 bp)

- RNA sequencing in small quantities (low input)

• Principle: enrichment of total RNA, depletion of abundant transcripts with AnyDeplete technology (ribosomes, globins etc.), ligation of Illumina adapters and PCR amplification.
• Amount of total RNA: 10 pg – 10 ng (1 – 500 cells)
• Recommended RNA quality: RIN > 8
• Kit Used: Ovation SoLo RNA-Seq (NuGEN)
• Sequencer: NextSeq500 (2 x 75 bp)

For this service, GENOM'IC also offers to perform the step of extracting total RNA from a suspension of a few hundred cells. Contact us.

In practice:

For all requests, contact us directly by e-mail  or on 01 40 51 65 65.

The core facility offers SNP genotyping services based on Affymetrix technology. It has a GCS3000 7G station with three fluidic stations and three hybridization ovens.
From the genomic DNA provided by the customer (accompanied by its QC), the service includes the production of raw data and their quality control.
The facility offers all types of Affymetrix genotyping arrays (SNP6 – human and murine, 750K, 250K, Oncoscan HD and Cytoscan HD).

In practice:

Contact us directly by e-mail or on 01 40 51 65 65.

GENOM'IC offers different DNA sequencing services (human exome, targeted, de novo) or DNA-Seq based on the use of NextSeq 500, Miseq from Illumina and S5 from Ion Torrent.

From the DNA provided by the customer (accompanied by its QC), the service includes the production of the libraries, their sequencing and the QC of the raw data. The sequencing approaches (single or paired readings, reading depth, Illumina or Ion torrent technology) are flexible and adaptable depending on the project. Each project will be the subject of an estimate adapted to the project and taking into account these different aspects.

The various DNA-Seq services offered include the preparation and sequencing of the bank from the DNA provided by the customer and checked by him.

For the analysis of exome and targeted data, the bioinformatics platform of the Université Paris Cité (directed by J-P. Jais and P.Nitschke) has a strong experience of this type of analysis and can put their analysis solution is available (contact us)

We distinguish :

human exome sequencing

The platform offers two exome services:

• a standard exome with the following specifications: mean target coverage between 60-80X and 90% of target bases > 20X
• a deep exome with the following specs: average target coverage between 150X and 80% of target bases > 50X
• Principle: after mechanical fragmentation (ultrasound), preparation of libraries then capture (SeqCap EZ MedExome Enrichment kit from Roche)
• Amount of DNA needed: 100 ng - 1 µg
• Kit used: Kapa Hyper (Kapa Biosystems)
• Sequencer: NextSeq 500 (2 x 75 bp)

targeted sequencing

The platform offers targeted sequencing services:

after multiplex PCR (ThermoFisher's AmpliSeq® technology followed by sequencing on S5): this technology is based on amplicon design (by Ion AmpliSeq Designer™) with amplicon sizes between 140 and 375 bp depending on the qualities of Starting DNA (respectively standard DNA and DNA extracted from FFPE cut)

• DNA quantity: 1 ng – 100 ng
• Kits used: Ion AmpliSeq™ Library 2.0 + Ion PGM™ Hi-Q™ OT2 and Hi-Q™ sequencing (ThermoFisher)
• Sequencer: S5XL

after targeted capture (SeqCapEZ Choice and EZ developerEnrichment capture technology from Roche)
Kit used: Kapa Hyperprep (KapaBiosystems)

• Sequencer: NextSeq 500 (up to 2 x 150bp) or Miseq (up to 2 x 300bp)

de novo sequencing

The core facility offers a de novo sequencing service:
After mechanical fragmentation (ultrasound), preparation of the libraries

• Amount of DNA needed: 100 ng - 1 µg
• Kit used: Kapa Hyper (Kapa Biosystems)
• Sequencer: NextSeq 500 (up to 2 x 150bp) or Miseq (up to 2 x 300bp)

In practice:

For all requests, contact us directly by e-mail  or on 01 40 51 65 65.

The core facility offers an immunoprecipitated chromatin sequencing service or ChIP-Seq based on the use of Illumina NextSeq 500.

From the DNA provided by the collaborator (accompanied by the photo of the gel), the basic service includes the quality control of the samples, the preparation of the banks, the sequencing and the quality control of the raw data. The sequencing approaches (single or paired readings, depth of readings) are flexible and adaptable according to the project. Each project will be the subject of an adapted estimate taking into account these different aspects.

Immunoprecipitated Chromatin Sequencing:

• Principle: repair of immunoprecipitated DNA fragments, ligation of Illumina adapters then amplification by PCR.
• DNA quantity: 100 pg – 50 ng
• Recommended fragment size: < 1000 bp (ideally between 200 and 600 bp)
• Kit Used: MicroPlex v2 (Diagenode)
• Sequencer: NextSeq 500 (1 x 75 bp or 2 x 40 bp)

In practice:

For all requests, contact us directly by e-mail  or on 01 40 51 65 65.

As part of its transcriptomic analyses, GENOM'IC produces and validates its data using quality controls adapted to each technique. This control ensures the quality of the data provided to the customer. GENOM'IC then performs the statistical analysis of the data.

For DNA chips, the basic service includes the production and analysis of data. Unsupervised and supervised analyzes are carried out in order to identify any technical biases or aberrant samples that could interfere with the analysis. The facility's experience in this area allows individualized analysis of each project. A file summarizing these different points and the lists of differentially expressed genes is provided to the client, accompanied by documents explaining the statistical methodology used. The facility is available to discuss and explain these different points to the client. GENOM'IC provides a text of materials and methods for future scientific publication.

For RNA-seq, a bioinformatics analysis service - including the steps of alignment, quality control of alignments and differential analysis (allowing to obtain a list of differentially expressed genes) - is offered to customers. The service includes

• the alignment work, the provision to the client of an analysis report summarizing the various quality controls of this alignment, accompanied by explanatory documents of the various metrics calculated.
• the analysis work, the provision to the client of an analysis report summarizing the various quality controls carried out, accompanied by documents explaining the statistical methodology used.

For the single-cell RNA-Seq, the platform offers a first analysis with the cellranger software, whose version and parameters are adapted to the protocol used for each project. This service includes

• alignment and quality controls for each sample, with an explanatory web report
• a first clustering of the cells with:
• A file usable by the team with the Loupe Browser software offered by 10X Genomics
• A set of raw or filtered matrices usable in R, with the Seurat package for example

The facility remains available to discuss and explain these different points to the client, and provides a text of materials and methods for future scientific publication.

GENOM'IC also offers its services for the graphic representation of results (such as Heatmaps or volcano plots for example) or for specific bioinformatics analyzes of a project. In the latter case, the possibility or not of carrying out a specific analysis or developing new pipelines is assessed according to the availability of staff and an estimate of the analysis is proposed.

For genomic analyzes like targeted sequencing, SNP analysis, GENOM'IC does not provide analysis. However, for particular projects, an adapted analysis can be envisaged according to the availability of the personnel and an estimate estimate of the analysis is proposed.

The core facility provides teams from Institut Cochin with four LightCycler® 480 (Roche). It updates software, monitors and maintains devices. This provision is made in the form of 1h30 reservation slots made on the Institut Cochin website.

GENOM'IC trains about fifty users each year in the real-time PCR technique and in the handling of LC480s in the form of monthly training sessions:

• mandatory LC480 training for new users (carried out on the LC480 Dogmatix on the 7th floor Roussy room 723 from 10:30 a.m. to 12 p.m. on Fridays)
• optional theoretical training: initiation and improvement in real-time PCR (Amphitheater G Roussy 1st basement from 2 p.m. to 4:30 p.m. on Fridays)

You will find at the following link the form to fill in to follow a training:

 Training LC480 

Theoretical training

Registration must be done no later than the Wednesday preceding the training.

GENOM'IC performs the extraction and quality control of total RNA from samples containing a limited number of cells (from 1000-2000 cells), after cell sorting for example.

In practice:

The facility provides a 1.5 ml tube containing a lysis buffer to the customer. The latter sorts these cells and immediately freezes the tube at -80°C. He then brings this dry ice tube to the facility for extraction, along with an excel spreadsheet summarizing the sample name and the number of sorted cells in the tube. In return, the facility provides a QC report of the total RNA extracted.

The service is called "small sample RNA extraction".

For certain projects, GENOM'IC can carry out the extraction and quality control of genomic DNA, total RNA or small RNA from all types of samples. Contact us for more information.

GENOM'IC deals with single cell and single nuclei projects for various applications (RNA-seq, ATAC seq, B and T repertoire, CITE-seq) based on 10X technology in partnership with CYBIO, the cytometry core facility of Institut Cochin. The cell and nuclear preparation steps are performed by CYBIO; GENOM’IC supports library preparation and sequencing, standard data analysis (analysis obtained from the 10X Cell Ranger suite). A more in-depth analysis can be considered depending on the availability of staff and is the subject of an estimate.

In practice:

Any team interested in a single cell analysis must complete an information sheet automatically transmitted to the CYBIO and GENOM'IC facilities.

Each request will be assessed by the platforms and a response will be given to the team within a maximum of 2 weeks. In the event of a favorable response, all the information necessary for the implementation of the project will be communicated to the team.