Interdisciplinary Centre Luxembourg Centre for Systems Biomedicine (LCSB)

Genomics Platform

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The Genomics Platform at the Luxembourg Centre for Systems Biomedicine (LCSB) is a research infrastructure dedicated to next-generation sequencing and genomic analysis. The platform provides sequencing services through access to advanced Illumina and Oxford Nanopore Technologies instruments, validated workflows, and expert technical support. The team supports research projects from experimental design and sample preparation to library preparation, sequencing, and bioinformatics analysis, maintaining rigorous quality standards throughout. For new users and projects, the platform offers consultation on experimental design and best practices, providing guidance on sample collection, DNA/RNA extraction, nucleic acid quality, biological replication, sequencing depth, and other key factors to ensure high-quality, reliable sequencing data.

The platform collaborates with academic and industrial partners to provide high-quality sequencing services, expert support, and reproducible genomic data that advance biomedical research.

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

  • iSeqTM 100 (Illumina)

    The iSeq鈩 100 is a compact benchtop sequencer from Illumina庐, Inc., designed for small-scale next-generation sequencing projects. It is well suited for applications such as amplicon sequencing, targeted sequencing, small genome sequencing, and sequencing library quality assessment.

    The system provides a simple and flexible workflow, generating up to approximately 4 million paired-end reads and up to 1.2 Gb of sequencing data per run, with read lengths of up to 2 脳 150 bp. Its rapid turnaround time and cost-effective operation make it an ideal solution for pilot studies, method development, and low-throughput sequencing projects.

  • 狈别虫迟厂别辩2000鈩

    狈别虫迟厂别辩2000鈩 is a benchtop as well as production scale sequencer from Illumina庐, 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鈩 sequencer, 狈别虫迟厂别辩2000鈩 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.

  • 惭颈苍滨翱狈庐
    (Oxford Nanopore)

    惭颈苍滨翱狈庐 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.
    惭颈苍滨翱狈庐 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 X

    The Chromium X from 10x Genomics is a high-throughput microfluidics platform designed for single-cell and single-nucleus analysis. It enables the generation of high-quality libraries for a wide range of applications, including single-cell gene expression, immune profiling, chromatin accessibility (scATAC-seq), multiome analysis, and other single-cell multiomics workflows.

    Using microfluidic partitioning, the Chromium X system efficiently captures thousands to tens of thousands of individual cells or nuclei in a single run, enabling comprehensive characterisation of complex biological samples at single-cell resolution. Its scalable workflow and compatibility with multiple assay types make it a versatile platform for large-scale single-cell genomics studies.

  • PromethION (Oxford Nanopore)

    The PromethION鈩 2 i is a compact, high-throughput nanopore sequencing platform from Oxford Nanopore Technologies, designed for real-time analysis of DNA and RNA. It is well suited for applications such as whole-genome sequencing, long-read transcriptomics, metagenomics, structural variant analysis, epigenetic profiling, and de novo genome assembly.

    Single flow cell can generate hundreds of gigabases of sequencing data in real time, with read lengths ranging from several kilobases to ultra-long reads exceeding 1 Mb, depending on sample quality and library preparation. This flexibility makes the PromethION 2 i an ideal platform for both medium- and high-throughput long-read sequencing projects.

Sample request

Please submit your sequencing and single cell project online using

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 >10碌l 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: 5-15碌g (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 >10碌l of sample
  8. minimum amount: 1碌g
  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: >10碌l
  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 .

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 . 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 糖心Vlog 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.

鈥淭he sequencing experiments presented in this paper were carried out at the LCSB sequencing platform (RRID: SCR_021931) at the 糖心Vlog鈥

OR

鈥淭he single cell sequencing experiments presented in this paper were carried out at the LCSB sequencing platform (RRID: SCR_021931) at the 糖心Vlog鈥

People

  • Dr. Rashi HALDER

    LCSB
    Research scientist
    Learn more

  • Janine SCHULZ

    LCSB
    Research Support Technician
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  • 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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