Bioinformatics Core Facility at Aarhus University: Services and Contact Details

The Bioinformatics Core Facility at Aarhus University offers bioinformatics training, consultation, data analysis, research collaboration, and more services for scientists. They provide expertise in NGS analyses, data formatting, knowledge dissemination, and pricing models. Contact them for bioinformatics solutions and collaborations.

• Bioinformatics
• Aarhus University
• Data Analysis
• Research Collaboration
• NGS Analyses

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1. Core Facility | Bioinformatics Department of Biomedicine Bulk RNA-sequencing workshop 10:30 19.01.2023 1116, 448A Associate Professor Per Qvist Research assistant Jacob Egemose H gfeldt

2. The Bioinformatics Core Facility The Bioinformatics Core Facility Established autumn 2022 Aim: to provide basic bioinformatics training, services as well as full-scale scientific collaborations for all scientists at Aarhus University as well as external academic and industrial partners. o One priority is to provide biologist-friendly solutions in order to implement the use of OMICs and other large-scale data at the Department of Biomedicine . Core activities: o Data analysis o Consultation o Training o Research collaboration o Knowledge dissemination o Fundraising

3. Services Services Consultation o Experimental design, bioinformatics methods and computational tools Data analysis o NGS analyses (e.g. RNAseq (bulk, spatial and single cell), ChIPseq, DNAseq (WGS and WES)) o DNA analyses (e.g. Functional annotations and geneset enrichment/association analyses) o RNA analyses (e.g. Expression profiling, target prediction, splicing) o Sequence analysis (e.g. variant detection, SNP annotation, Transcription factor binding sites) Data formatting/structuring o Preparation of data for public repositories (Open Science) Data mining o OMICs data Knowledge dissemination o Assistance in preparation of manuscripts, presentations and grant proposals Training o Workshops on Bioinformatics topics and data access/analysis o Open Office o Teaching o Supervision 04/10/202414/10/2022

4. Pricing model Pricing model Come by for a chat that is for free -Seminars -Data formatting -Customized requests -Workshops -Data processing -Biological interpretation PRODUCTS PROJECTS TRAINING Think Bioinformatics fee into grant proposals -Q&A -Mapping -Field-specific platforms -Open office -Annotation -Downstream targeted approaches We are not competing with other AU/non-AU service providers we complement -Supervision -DE analyses -etc -etc -Visualization -etc Collaboration Estimated cost Outsource Free DKK 450/h

5. CONTACT CONTACT Address o The Skou Building 1116, room 456 H egh-Guldbergsgade 10 8000 Aarhus C https://biomed.au.dk/bioinformatics-core-facility Denmark Open Office o You are free to come by for an initial discussion of your projects always and we attempt to keep the core open every Monday 10.30-12.00. However, we encourage you to call/write first and make an appointment. Core Facility Manager o Per.q@biomed.au.dk o 50192006 04/10/202414/10/2022

6. Agenda Transcriptomics Workflow of analysis Examples of quality controls Examples of work Do-it-yourself tutorial using galaxy

8. From biological experiment to computational science

9. Workflow: mRNA-seq Data Analysis

10. Workflow: mRNA-seq Data Analysis

11. Workflow: mRNA-seq Data Analysis

12. Workflow: mRNA-seq Data Analysis

13. Workflow: mRNA-seq Data Analysis

14. How to analyse? UNIX / Bash environment R / Python programming *Graphical user interface* Drag and drop Graphical user intefrace

15. Galaxy

16. Fast Quality Control (FastQC)

17. Per base sequence quality

18. Trimming

19. Fast Quality Control (FastQC)

20. Per base sequence content

21. Fast Quality Control (FastQC)

22. High GC content tendency

23. Per sequence GC content

24. Fast Quality Control (FastQC) fastqc_report.html

25. Alignment to a reference genome Standard reference genomes are pre-installed in galaxy. However, we recommend to download a complete assembly set from e.g., NCBI or Ensembl for exact workflow. Single-end or paired-end reads? Tools: STAR or HiSat2. Input files: FASTA files (.fq) + reference genome. Output files: Binary Alignment and Map files (.BAM).

27. Feature counts Used to measure gene expression from .BAM files. General feature Format (GFF) file is required. NCBI Assembly database. Tools: FeatureCount or StringTie. Input files: .BAM files + General Feature Format (GFF) file. Output files: Gene count tables.

28. Feature Count expectations

29. Differential expression gene analysis Determine differentially expressed features from feature count tables. Tools: DESeq2, EdgeR, Limma. Input files: Gene count tables. Output files: A variety of DEG plots.

30. DEG plots

31. DIY in Galaxy https://usegalaxy.eu/ US server, EU server, AUS server. .eu specify that you use a european server. https://www.ncbi.nlm.nih.gov/

32. AARHUS UNIVERSITY