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 and CyTOF Mass 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, usually state-of-the-art, instruments and services, and managed by scientists with the 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 |
Director of the Core Facility
|
013-28 25 98
|
vesa.loitto@liu.se
|
Building 462, entrance 54/71, floor 10, Campus US
|
| Service list |
| ► Bioinformatics (10) | |||
| Name | Description | Price | |
|---|---|---|---|
| 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.
IMPORTANT we ask you to be included as co-author(s) of papers that use these results since this analysis requires a substantial intellectual contribution. |
Internal
kr 1,500.00
Sample
External kr 3,000.00 Sample Corporate kr 2,000.00 Sample |
|
| 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.
IMPORTANT we ask you to be included as co-author(s) of papers that use these results since this analysis requires a substantial intellectual contribution. |
Internal
kr 520.00
each
External kr 800.00 each Corporate kr 600.00 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.
IMPORTANT we ask you to be included as co-author(s) of papers that use these results since this analysis requires a substantial intellectual contribution.
|
Internal
kr 1,000.00
Sample
External kr 1,500.00 Sample Corporate kr 1,250.00 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.
IMPORTANT we ask you to be included as co-author(s) of papers that use these results since this analysis requires a substantial intellectual contribution.
|
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.
IMPORTANT we ask you to be included as co-author(s) of papers that use these results since this analysis requires a substantial intellectual contribution.
|
Internal
kr 5,000.00
Sample
External kr 7,000.00 Sample Corporate kr 6,000.00 Sample |
|
| Bioinformatics: Illumina DNA Methylation Array Data Analysis (Standard Analysis) |
1. Quality control 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.
IMPORTANT we ask you to be included as co-author(s) of papers that use these results since this analysis requires a substantial intellectual contribution.
|
Internal
kr 2,500.00
Sample
External kr 4,000.00 Sample Corporate kr 3,500.00 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.
IMPORTANT we ask you to be included as co-author(s) of papers that use these results since this analysis requires a substantial intellectual contribution. |
Internal
kr 500.00
each
External kr 1,000.00 each Corporate kr 2,000.00 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.
IMPORTANT we ask you to be included as co-author(s) of papers that use these results since this analysis requires a substantial intellectual contribution. |
Internal
kr 3,000.00
each
External kr 5,000.00 each Corporate kr 4,000.00 each |
|
| Bioinformatics: Gene Expression Data Enrichment Analysis using iPathwayGuide (Licensed) (Performed by User) |
Gene Expression Data Enrichment Analysis (GO/Pathways/Networks) is performed by the User himself using iPathwayGuide. |
Inquire | |
| Bioinformatics: Gene Expression Data Enrichment Analysis using iPathwayGuide (Licensed) (Performed by Core Facility) |
Please email us if you have any question.
IMPORTANT we ask you to be included as co-author(s) of papers that use these results since this analysis requires a substantial intellectual contribution. |
Inquire | |
| ► Electron microscopy (1) | |||
| Name | Description | Price | |
| Microscope Set Up Fee | Inquire | ||
