Interdisciplinary Centre Luxembourg Centre for Systems Biomedicine (LCSB)

Genomics Platform

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The genomics platform at the LCSB offers next-generation sequencing services. The platform has a NextSeq2000 and a MiSeq sequencer from Illumina, and 2 MinION & Mk1c nanopore sequencer from Oxford Nanopore Technologies, which allow for high flexibility when it comes to different sequencing needs.
For first-time users as well as for researchers with new projects, we encourage to meet in person and discuss the project objectives and goals. It helps us understand your needs, which are almost unique for every project. Following our discussion, we offer our best advice and recommendations related to best practices to obtain the relevant and good quality sequencing data. Some of the points that we suggest considering for your sequencing projects are:
• How many samples (number) are necessary to obtain a robust result?
• How are these samples collected?
• Which DNA/RNA isolation technique is optimal?
• How is better RNA integrity achieved?
• How many biological replicates are necessary?
• How much sequencing data coverage (depth) is required?

Services

Transcriptomics:

  • Bulk RNA sequencing
  • Small RNA sequencing
  • Meta-transcriptomics sequencing

Genomics:

  • Whole genome sequencing (small genomes)
  • Chromatin immunoprecipitation sequencing (ChIP-Seq)
  • Methylated DNA immunoprecipitation sequencing (MeDIP-Seq)
  • Reduced representation bisulfite sequencing (RRBS)
  • Assay for Transposase-Accessible Chromatin sequencing (ATAC-Seq)
  • Exome-sequencing
  • Meta-genomics/ shotgun

Targeted Resequencing:

  • RNA (gene panel)
  • DNA (gene panel)
  • Amplicon sequencing

  • Metagenome sequencing
  • Whole genome sequencing
  • mtDNA sequencing
  • amplicon sequencing
  • full length 16S/18S rRNA sequencing
  • full length cDNA sequencing
  • direct RNA sequencing
    In case you have a project with an application not listed above, please contact us regarding the feasibility.

  • Drop-seq
  • 10X Genomics
    In case you have a project with an application not listed above, please contact us regarding the feasibility.

Equipment

  • MiSeq™ (Illumina)

    MiSeq™ is a benchtop sequencer from Illumina®, Inc. and is well suited for sequencing projects such as amplicon sequencing, targeted resequencing, and targeted gene expression profiling.
    The applications can be tuned to individual requirements as the MiSeq™ system along with its different reagent kits can offer up to 25 million reads per run and up to 15 Gb of sequencing data, with up to 2 x 300 bp read length.

  • NextSeq2000™

    NextSeq2000™ is a benchtop as well as production scale sequencer from Illumina®, Inc. and is well suited for sequencing projects requiring small genome whole-genome sequencing, exome sequencing, whole-transcriptome sequencing.
    With a higher throughput than MiSeq™ sequencer, NextSeq2000™ sequencer along with its different reagent kits can offer up to 1.2 billion reads per run and up to 360 Gb of sequencing data. The maximum read can be 2 x 300 bp.

  • MinION®
    (Oxford Nanopore)

    MinION® is a sequencer from Oxford Nanopore Technologies and offers the possibility to sequence DNA or RNA fragments of versatile lengths, even up to several hundred kilobases long fragments.
    MinION® sequencer is well suited for sequencing projects interested in de novo sequencing, targeted sequencing, metagenomics, transcriptome, and epigenetics. It can generate up to 50 Gb of data per flow cell (72 hrs of sequencing run).

  • 10X Chromium controller

    Chromium controller is the microfluidics-based device. With the use of Next GEM technology, it performs single cell partitioning and barcoding with 20 minutes. In a single channel one can generate up to 10,000-20,000 barcoded single cells.

Sample request

Please submit your sequencing and single cell project online using Calpendo

DNA/HMW-DNA

  1. same extraction protocol
  2. RNase Treatment
  3. OD260/280: 1.8, OD 260/230: between 1.8 and 2.0
  4. Solvent: nuclease free water or low TE (10mM Tris, 0.1 mM EDTA)
  5. provide >10µl of sample
  6. minimum amount:
    • ChIP DNA: 10ng
    • genomic DNA:
      • shotgun/WGS: 500ng (without PCR amplificaiton) and 50ng (with PCR amplification)
      • amplicon sequencing (16S/18S/ITS): 50ng
    • High molecular weight DNA: 5-15µg (please provide gel image)
  7. use 1.5ml leak-lock tubes (from Eppendorf or similar), for 16S/18S sequencing, in PCR plate.
  8. For sample submission in Calpendo nanodrop conc., 280/260 and 230/260 ratios information is mandatory

RNA

  1. same extraction protocol
  2. DNase Treatment
  3. OD260/280: 2, OD 260/230: between 1.8 and 2.0
  4. RIN value >7 or equivilent
  5. high/low MW rRNA ration ~2
  6. Solvent: nuclease free water
  7. provide >10µl of sample
  8. minimum amount: 1µg
  9. use 1.5ml leak-lock tubes (from Eppendorf or similar)
  10. For sample submission in Calpendo nanodrop conc., 280/260 and 230/260 ratios information is mandatory.

Note: All our protocols use totalRNA as starting material. In case you have mRNA, rRNA depleted RNA or smRNA please check with us before to confirm the compatibility with the protocol.

Prepared library

  1. Minimum concentration: 10nM
  2. Volume: >10µl
  3. Bioanalyzer report for individual libraries
  4. use 1.5ml leak-lock tubes (from Eppendorf or similar) or PCR plate

Samples not fulfilling the sample requirements will FAIL at the sample QC step and will not be processed further.

DNA/HMW-DNA

  1. Unique name
  2. Sample name can only have alphanumeric (a-z, 0-9), dash (-) and underscore (_) values.
  3. Date
  4. Submitter’s name
  5. Sample concentration

RNA

  1. Unique name
  2. Sample name can only have alphanumeric (a-z, 0-9), dash (-) and underscore (_) values.
  3. Date
  4. Submitter’s name
  5. Sample concentration

Prepared library

  1. Unique name
  2. Sample name can only have alphanumeric (a-z, 0-9), dash (-) and underscore (_) values.
  3. Date
  4. Submitter’s name
  5. Sample concentration

Please consult the general terms and conditions for platform services.

Before sample submission to the platform, sequencing project and sample information need to be submitted online at Calpendo.

You will be asked to provide an OTP in the billing/invoicing tab at the time of project creation. Please discuss with your PI which budget code to use. This will be used for internal invoicing after completion of the project. For external users the Purchase Order (PO) number need to be provided in the tab. Please send the soft copy of PO to LCSB-sequencing@uni.lu before sending samples for sequencing. The sample processing will start with the reception of the PO.

For more than one sample submission CSV (comma separated) file can be used. Template csv file can be downloaded for the DNA, RNA and Library or from Calpendo.

Please drop your samples in a dedicated tray in delivery freezer at BT1 room 501. The samples will be picked from the tray on Tuesday/Thursday after 16:00hrs. Incorrectly labeled boxes/samples will not be picked and might lead to unnecessary delays in the sample processing. Internal users who do not have access to BT1 building or room 501 can borrow the genomics platform access card from the guard present at the reception and return after dropping the sample box. External users (with in Luxembourg) can come for sample delivery on a prefixed date and time. For sample delivery via the post we suggest to post the package on Monday/Tuesday to minimise the risk of sample loss.

Single-cell projects

After the kick-off meeting the online samples submission is done using via Calpendo. For single cell sample processing is scheduled for pre-agreed date and time. The samples can only be process if the project is approved for the desired date and time. The facility will check the sample quality and might decide not to process the samples if the samples quality is not satisfactory. It is possible to process such samples if PI provides the written (via email) agreement to accept the risk and cover the costs.

Sequencing data transfer

Internal users with HPC access: Once the sequencing run is completed, the sequencing data is available to the University of Luxembourg researchers with the access to the internal computational resources via a folder sharing (group folder on Isilon)

External users/ users with no HPC access, we offer data transfer via (i) secured FTP link, or (ii) secured folder accessibility or (iii) user provided solution -like user OneDrive, ownCloud etc. For human samples encrypted data is shared using the asperaWEB (IBM) Server.

Invoicing

For internal users, the invoicing will be done via simple fund transfer request to SFC upon PIs approval. This invoicing is done quarterly. For external users, the final invoice for our services will be send electronically (via PEPPOL).

Acknowledgements

Please acknowledge the services provided by the sequencing platform in the resulted manuscript. Below is the example text.

“The sequencing experiments presented in this paper were carried out at the LCSB sequencing platform (RRID: SCR_021931) at the University of Luxembourg”

OR

“The single cell sequencing experiments presented in this paper were carried out at the LCSB sequencing platform (RRID: SCR_021931) at the University of Luxembourg”

People

  • Dr. Rashi HALDER

    Dr. Rashi HALDER

    LCSB
    Research scientist
    Learn more
  • Janine SCHULZ

    Janine SCHULZ

    LCSB
    Research Support Technician
    Learn more
  • Paula-Cristina LUPU

    Paula-Cristina LUPU

    LCSB
    Research and development specialist
    Learn more

Contact

For any inquiries or questions regarding methodologies, instrumentation, sample processing, or prices, we invite you to contact us via email or phone.

  • LCSB-sequencing@uni.lu

  • (+352) 466 644 6189

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