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Schedule 
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    :local:



Monday (22 September 2025)
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**DNA methylation with Illumina array and Bisulfite-seq**

**09:00 - 09:30** Welcome

**09:30 - 10:15** Introduction to DNA methylation + Overview Array Exercises

**10:15 - 10:30** :doc:`Uppmax set up <./tutorials/setup/lab-setup>` + break

**10:30 - 12:00** :doc:`Exercises Array Workflow <./tutorials/methylationArray/Array_Tutorial>`

**12:00 - 13:00** lunch *(offline)*

**13:00 - 14:00** Methylation methods & technologies (Jessica Nordlund)

**14:00 - 14:15** Break

**14:15 - 14:30** Methylation Exercises Overview II: Methylation Sequencing

**14:30 - 16:00** :doc:`Exercises Methylation Sequencing <./tutorials/methylationSeq/Seq_Tutorial>`

**16:00 - 17:00** Daily challenge *(offline)*


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Tuesday (23 September 2025)
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**ATAC-seq: data processing and analysis principles**


**09:00 - 09:30** Recap previous day 

**09:30 - 10:15** Introduction to ATAC-seq data analysis  

**10:30 - 11.30** :doc:`Exercise: Data preprocessing and general QC <./tutorials/data-preproc-tutorials>`
and :doc:`ATACseq QC <./tutorials/data-preproc/data-qc-atac>` 

**11:30 - 12:00** :doc:`Exercise: ATAC-seq data analysis <./tutorials/ATACseq/lab-atacseq-bulk>` 

**12:00 - 13:00** lunch *(offline)*

**13:00 - 13.45** Presentation and Q&A with National Genomics Infrastructure (Orlando Contreras Lopez and Michelle Ljungmark)

**13:45 - 14:00** Break

**14:00 - 15:30** :doc:`Exercise: ATAC-seq data analysis <./tutorials/ATACseq/lab-atacseq-bulk>` 

**15:30 - 17:00** Exercise *(offline support)*

**16:00 - 17:00** Daily challenge *(offline)*





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Wednesday (24 September 2025)
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**New methods and quantitative ChIP-seq** (Simon Elsässer and Carmen Navarro Luzón)

**09:00 - 10:00** Recap previous day 

**10.00 - 11.00** ChIP-seq methods  

**11.00 - 12.00** ChIP-seq alternatives  

**12:00 - 13:00** lunch *(offline)*

**13:00 - 13:30** Introduction to exercises  

**13:30 - 16:00** :doc:`Principles of ChIP-seq <./tutorials/chipseqProc/lab-chipseq-processing>`
and :doc:`Advanced ChIP Methods <./tutorials/quantitative_chip_tutorials>` 

**16:00 - 17:00** Exercises *(offline support)*

**16:00 - 17:00** Daily challenge *(offline)*



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Thursday (25 September 2025)
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**Downstream analyses**

**09:00 - 09:30** Recap previous day 

**09:30 - 10:00** Introduction to transcription factors and gene regulation *(slides)*

**10:00 - 10:30** Exercises: :doc:`Representing transcription factor binding sites <./tutorials/motifAnalyses/representingMotifs>` *(online session)*

**10:30 - 10:45** break *(offline)*

**10:45 - 12:00** Exercises: :doc:`Predicting relevant motifs <./tutorials/motifAnalyses/motifAnalysesWithMonalisa>` *(online session)*

**12:00 - 13:00** lunch *(offline)*

**13:00 - 15:00** :doc:`Additional downstream exercises <./tutorials/downstream_tutorials>` *(online support)*

.. and :doc:`genome overlaps <./tutorials/downstream_tutorials>` *(online support)*

**15:00 - 17:00** Exercises *(offline support)*

**16:00 - 17:00** Daily challenge *(offline)*



Friday (26 September 2025)
--------------------------------

**Integrative and single cell omics**

**09:00 - 09:30** Recap previous day 

**09.30 - 10.20** Single cell methods 

**10.20 - 10.35** Break

**10.35 - 11.15** Integration of genomics data 

**11:15 - 11:20** Introduction to exercises 

**11.20 - 12.00** :doc:`Single cell and data integration exercises <./tutorials/data_integration_tutorials>` 

.. and :doc:`optional exercise on Multi-OMICs Factor Analysis <./tutorials/unsupervised_data_integration/lab-unsupervised_data_integration>` 


**12:00 - 13:00** lunch (offline)


**13.00 - 14.00** :doc:`Single cell and data integration exercises <./tutorials/data_integration_tutorials>` 

.. and :doc:`optional exercise on Multi-OMICs Factor Analysis <./tutorials/unsupervised_data_integration/lab-unsupervised_data_integration>` 


**14.00 - 15.00** Inspirational talk: Marek Bartosovic (Stockholm University).  
`Deciphering the epigenetic landscape of the brain: Innovations in chromatin profiling with single-cell nano-CUT&Tag <https://www.scilifelab.se/event/big-talk-deciphering-the-epigenetic-landscape-of-the-brain-innovations-in-chromatin-profiling-with-single-cell-nano-cuttag/>`_.  Join by `Zoom <https://lu-se.zoom.us/j/62767371752>`_.



**15:00 - 16:00** Daily challenge  

**15:00 - 16:00** `Short term feedback form <https://forms.gle/qdN8M87oqHkgtQC8A>`_

**15.00 - 16.00** Course wrap-up



.. Add links to slides like this: (slides copied to directory slides)

.. `Methylation Introduction Slides <../_static/Methylation_Slides.pdf>`_

.. `DNA Methylation Methods and Technologies (Jessica Nordlund) <../_static/JN-EpigeneticsMethods_2021-10-25.pdf>`_

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