Welcome!
Core Facility at the Faculty of Medicine and Health Sciences at Linköping University is a research infrastructure and consists of several platforms that provide a cost-effective access to advanced instrumentation, training, consulting and qualified specialized services withing following areas: Mass Spectrometry; Flow Cytometry; Molecular biology; Microscopy; and Bioinformatics. Core Facility is a collaboration between the Faculty of Medicine and Health Sciences and the Region Östergötland. Our specialized laboratories are equipped with unique, mostly state-of-the-art, instruments. Services are managed by scientists with both technical expertise and research experience to help another researcher. Core Facility is open to all internal and external research groups.
Vesa Loitto | Head of Core Facility |vesa.loitto@liu.se
Ana Maria Carrasco Del Amor | Mass Spectrometry | ana.carrasco@liu.se
Mouna Tababi | Molecular Biology | mouna.tababi@liu.se
Åsa Schippert | Molecular Biology | asa.schippert@liu.se
Vesa Loitto | Microscopy and Image Processing | vesa.loitto@liu.se
Maria Ntzouni | Electron Microscopy and Histology | maria.ntzouni@liu.se
Mikael Pihl | Flow Cytometry and CyTOF | mikael.pihl@liu.se
Jörgen Adolfsson | Flow Cytometry and CyTOF | jorgen.adolfsson@liu.se
Jyotirmoy Das | Bioinformatics | jyotirmoy.das@liu.se
Leila Nasirzadeh | Bioinformatics | leila.nasirzadeh@liu.se
Massimiliano Volpe | Bioinformatics | massimiliano.volpe@liu.se
Linköping University, Faculty of Medicine and Health Sciences, Campus US Core Facility, LiU
Prior to booking and using the facility resources, new and prospective users must consult with the Core Facility staff concerning operating policies, training, access to our laboratories and discuss the specifics of the experiments. We are available to advise users regarding proper sample preparation for various applications and can provide relevant experimental protocols. Established users sign up for instrument time via booking calendar. Core Facility personnel can assist with acquisition setup and provide troubleshooting assistance. Development of new applications is encouraged, and research collaboration is feasible. After your experiment has been completed, the Core Facility personnel may assist you with the analysis of the results and manuscript preparations if requested. Training sessions are available for large-scale projects.
All users must acknowledge the Core Facility in publications that include data generated at the Core Facility. Guidelines.
What to always include:
“We acknowledge the Core Facility at the Faculty of Medicine and Health Sciences, Linköping University for providing assistance in [technology...].”
Significant help from a specific researcher at the Core Facility and acknowledgement by name:
“The authors thank Dr [name] at the Core Facility at the Faculty of Medicine and Health Sciences, Linköping University for [support and guidance in…].”
Substantial contributions that merit co-authorship of papers
If scientists from the Core Facility contribute more than routine techniques and when they make a substantial intellectual and/or experimental contribution to a research study, they should be co-authors of papers that use these data. These applies to: (1) Intellectual contribution, concept, design of project, critical input, and original ideas: (2) Data analysis and interpretation, preparation of figures and tables for publications; (3) Write a portion of the paper, draft the article, or revise it critically for intellectual content. Authorship is preferably established at the beginning of the project so that both the user e.g. the PI and the Core Facility researcher are aware of each other’s criteria.
Charging for services does not preclude acknowledgement for support or co-authorship
| Name | Role | Phone | Location | |
|---|---|---|---|---|
| Vesa Loitto |
Head of Core Facility
|
070-145 31 17
|
vesa.loitto@liu.se
|
Building 462, entrance 54/71, floor 10, Campus US
|
| Service list |
| ► Bioinformatics (12) | |||
| Name | Description | Price | |
|---|---|---|---|
| Bioinformatics: Illumina DNA Methylation Array Data Analysis (Standard Analysis) |
1. Quality control 2,750 SEK for per pairwise comparison (e.g., Group A vs Group B) anlysis (up to 20 samples per group). Each additional sample per group will cost next 2,750 SEK.
Details can be found in the request form. Please email us if you have any question.
With standard pipeline, tables in CSV or Excel file and figures in PNG or JPEG format.
*Additional Customizations on hourly basis.
|
Internal
kr 2,750.00
Sample
External kr 4,400.00 Sample Corporate kr 4,000.00 Sample |
|
| Bioinformatics: DNA Methylation Array Data Analysis (Illumina) - Custom Analysis |
With the standard DNA Methylation Data Analysis from Illumina EPIC arrays (EPICv1 and EPICv2), Bioinformatics Unit can also perform following analysis with additional costs - EACH ANALYSIS COSTS 500 SEK 1. DNA Methylation Age Prediction (using Horvath (2013), Hannum (2013) and Zhang (2019) ) 2. Cell type estimation 3. Differential Methylation regions identification 4. Copy-Number Variation Analysis against TCGA dataset and Tumor purity estimation. 5. Manhattan plot + region specific plot (max. 5 regions) 6. Principal Component Regression Analysis (PCR) with covariates 7. Gene Ontology (GO) Enrichment Analysis - Biological Processes, Molecular Function and Cellular Components 8. Biological Pathways Enrichment Analysis with Pathway Maps (max. 5 pathways) using KEGG database
1. Send a brief details of your query. 2. Job hour will be decided by the Bioinformtics Unit, Core Facility. 3. Upload raw data to the server/SharePoint/OneDrive/Central Storage. No USB. 4. Acknowledgement in the publication is a requirement. Generating Figures for the manuscript requires authorship and the author position should be discussed before. 5. This service only allows a single, short job and not listed on other service failities in the Bioinformatics Unit available. 6. Please note that your data and results will be deleted from our server after 7 days of job completion.
Please email us if you have any question.
With standard pipeline, tables in CSV or Excel file and figures in PNG or JPEG format.
*Additional Customizations on hourly basis.
|
Internal
kr 550.00
each
External kr 1,100.00 each Corporate kr 2,200.00 each |
|
| Bioinformatics: DNA Methylation Sequencing Data Group Analysis (Illumina/Nanopore/Twist/PacBio) |
1. Quality control COST PER SAMPLE
With standard pipeline, tables in CSV or Excel file and figures in PNG or JPEG format.
*Additional Customizations on hourly basis.
(From Human, Bacteria and Viruses)
Please email us if you have any question.
|
Internal
kr 3,300.00
each
External kr 5,500.00 each Corporate kr 4,400.00 each |
|
| Bioinformatics: DNA Methylation Sequence Data Analysis - Custom Analysis |
With the standard DNA Methylation Data Analysis from Illumina, Nanopore, Twist and PacBio, Bioinformatics Unit can also perform following analysis with additional costs - EACH ANALYSIS COSTS 800 SEK 1. DNA Methylation Age Prediction (using Horvath (2013), Hannum (2013) and Zhang (2019) ) 2. Cell type estimation 3. Differential Methylation regions identification 4. Copy-Number Variation Analysis against TCGA dataset and Tumor purity estimation. 5. Manhattan plot + region specific plot (max. 5 regions) 6. Principal Component Regression Analysis (PCR) with covariates 7. Gene Ontology (GO) Enrichment Analysis - Biological Processes, Molecular Function and Cellular Components 8. Biological Pathways Enrichment Analysis with Pathway Maps (max. 5 pathways) using KEGG database 9. Brain Tumor Methylation Classifier using NanoDx (for nanopore data only) 10. Heidelberg Brain Tumor Classifier for Illumina Array Data
1. Send a brief details of your query. 2. Job hour will be decided by the Bioinformtics Unit, Core Facility. 3. Upload raw data to the server/SharePoint/OneDrive/Central Storage. No USB. 4. Acknowledgement in the publication is a requirement. Generating Figures for the manuscript requires authorship and the author position should be discussed before. 5. This service only allows a single, short job and not listed on other service failities in the Bioinformatics Unit available. 6. Please note that your data and results will be deleted from our server after 7 days of job completion.
Please email us if you have any question.
With standard pipeline, tables in CSV or Excel file and figures in PNG or JPEG format.
*Additional Customizations on hourly basis.
|
Internal
kr 900.00
each
External kr 1,400.00 each Corporate kr 2,200.00 each |
|
| Bioinformatics: Microarray Data Analysis (Standard Analysis) |
1. Quality control
With standard pipeline, tables in CSV or Excel file and figures in PNG or JPEG format.
*Additional Customizations on hourly basis.
Please email us if you have any question.
|
Internal
kr 1,100.00
Sample
External kr 1,650.00 Sample Corporate kr 1,400.00 Sample |
|
| Bioinformatics: RNA-seq Gene Expression Data Analysis (Standard Analysis) |
Quality Control, Adapter and quality trimming, Genome indexing, Alignment, Sort and index alignments, Quantification, Identification of differentially expressed genes - 2,500 SEK for per pairwise comparison (e.g., Group A vs Group B) anlysis (up to 20 samples per group). Each additional sample per group will cost next 2,500 SEK.
Details can be found in the request form. Please email us if you have any question. With standard pipeline, tables in CSV or Excel file and figures in PNG or JPEG format.
*Additional Customizations on hourly basis.
|
Internal
kr 2,500.00
Sample
External kr 5,000.00 Sample Corporate kr 4,000.00 Sample |
|
| Bioinformatics: Single-Cell RNA Sequencing Data Analysis (10X Genomics) |
Quality Control, mapping, processing to UMAP/t-SNE, identification of markers - 30,000 SEK for up to 8 samples. Each additional sample will cost 5000 SEK. *Cell-type annotation and Differential Expression analysis will be charged 5000 SEK. With standard pipeline, tables in CSV or Excel file and figures in PNG or JPEG format.
*Additional Customizations on hourly basis.
Please email us if you have any question.
|
Internal
kr 5,000.00
Sample
External kr 7,000.00 Sample Corporate kr 6,000.00 Sample |
|
| Bioinformatics: Shotgun Metagenomics Data Analysis . Assembly, AMR and Plasmid Detection (Standard Analysis) |
1. Quality control 2. Read trimming and filtering Host DNA removal 3. Host DNA removal 4. De novo assembly 5. Taxonomic classification 6. Antimicrobial resistance (AMR) gene detection 7. Plasmid detection and characterization
2700 SEK up to 20 samples per project. Each additional sample will cost 3,500 SEK. Details can be found in the request form. Please email us if you have any question.
With standard pipeline, tables in CSV or Excel file and figures in PNG or JPEG format. Long read data additionally includes an interactive HTML comprehensive report.
*Additional Customizations on hourly basis. |
Internal
kr 2,700.00
each
External kr 4,300.00 each Corporate kr 4,000.00 each |
|
| Bioinformatics: 16S rRNA Amplicon Sequencing Data Analysis (Standard Analysis) |
1. Quality control
2,500 SEK per pairwise comparison (e.g., Group A vs Group B) analysis (up to 20 samples per group). Each additional sample per group will cost next 2,500 SEK. Details can be found in the request form. Please email us if you have any question.
With standard pipeline, tables in CSV or Excel file and figures in PNG or JPEG format.
*Additional Customizations on hourly basis. |
Internal
kr 2,500.00
each
External kr 4,000.00 each Corporate kr 3,700.00 each |
|
| Bioinformatics: Metabolomics data analysis (Standard) |
1. Quality control
With standard pipeline, tables in CSV or Excel file and figures in PNG or JPEG format.
*Additional Customizations on hourly basis.
Please email us if you have any question.
|
Internal
kr 1,650.00
Sample
External kr 3,300.00 Sample Corporate kr 2,200.00 Sample |
|
| Bioinformatics: nf-core Pipeline Execution Service |
Check nf-core pipelines for RNAseq, WGS, WES, scRNAseq, ChIPseq and many others 1. User-defined nf-core pipeline execution 2. Pipeline run on dedicated HPC resources (CPU or GPU) 3. Upload input data and other necessary file via NIMBUS Data Delivery System (https://nimbus.research.liu.se) 4. Results will be uploaded to user project folder on nimbus once the run complete with a runtime log.
Pricing: - Running on CPU (max 64 cores; 512GB RAM):250 SEK/24hr (Double rate applies if runtime exceeds 36 hrs.)
- Running on single L40S GPU (VRAM 48GB) + 16 cores on CPU: 1,000 SEK/12hr
- Running on 2x L40S GPUs (VRAM 2x48GB) + 16 cores on CPU: 1,500 SEK/12hr
- Customized resource request should be pre-discussed (subject to availability)
Note to remember:
- GPU jobs are strictly limited to 12 hours maximum runtime
- Users are responsible for providing a valid samplesheet and pipeline parameters.
- Results are delivered as-is from the pipeline output.
- Maximum runtime for a single pipeline: 160 hrs (can be resumed, if necessary)
Please email us if you have any questions corefacility_liu@liu.se or clinical.genomics@liu.se.
|
Internal
kr 250.00
each
External kr 500.00 each Corporate kr 400.00 each |
|
| Bioinformatics: Custom Bioinformatics services |
We offer some basic and advance bioinformatics solution on a per hour charge. Results - Tables and Figures can be in various format (as per request). *Maximum 40 hours per project can be booked. More than 40 hours, will be put on the queue (results in delay to deliver analysis result).
Please email us if you have any question.
|
Internal
kr 600.00
each
External kr 900.00 each Corporate kr 750.00 each |
|
| ► Electron microscopy (1) | |||
| Name | Description | Price | |
| Microscope Set Up Fee | Inquire | ||
