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--- # ChIP-seq data analysis --- ## Requirements Before diving into this slide deck, we recommend you to have a look at: - [Introduction to Galaxy Analyses](/archive/2020-12-01/topics/introduction) - [Sequence analysis](/archive/2020-12-01/topics/sequence-analysis) - Quality Control: [
slides](/archive/2020-12-01/topics/sequence-analysis/tutorials/quality-control/slides.html) - [
hands-on](/archive/2020-12-01/topics/sequence-analysis/tutorials/quality-control/tutorial.html) - Mapping: [
slides](/archive/2020-12-01/topics/sequence-analysis/tutorials/mapping/slides.html) - [
hands-on](/archive/2020-12-01/topics/sequence-analysis/tutorials/mapping/tutorial.html) .footnote[Tip: press `P` to view the presenter notes] ??? Presenter notes contain extra information which might be useful if you intend to use these slides for teaching. Press `P` again to switch presenter notes off Press `C` to create a new window where the same presentation will be displayed. This window is linked to the main window. Changing slides on one will cause the slide to change on the other. Useful when presenting. --- ### <i class="far fa-question-circle" aria-hidden="true"></i><span class="visually-hidden">question</span> Questions - What is ChIP-seq? --- ### <i class="fas fa-bullseye" aria-hidden="true"></i><span class="visually-hidden">objectives</span> Objectives - Identify ChIP-seq data --- ## ChIP-seq - **Ch**romatin **I**mmuno**P**recipitation combined with **seq**uencing - Identifying the location of proteins binding sites - Transcription Factors - Histone modifications - 2 Types of sequenced data - ChIP data - Input data .image-75[!(../../images/formation_of_super-structures_on_xi/chipseq.png)] --- ## Generating ChIP-seq data !(../../images/formation_of_super-structures_on_xi/chipseq_generation.png) <small> Source: [Wikipedia](https://en.wikipedia.org/wiki/ChIP-sequencing ) </small> --- ## ChIP vs Input !(../../images/formation_of_super-structures_on_xi/chip_vs_input.png) --- !(../../images/formation_of_super-structures_on_xi/chipseq_pipeline.png) --- ## Studying the effect of SCHMD1 protein in chromosome X SCHMD1 in known to have an effect on gene expression in X chromosome !(../../images/formation_of_super-structures_on_xi/SCHMD1.png) Chen-Yu Wang et al. 2018; Vivek Bhardwaj, Steffen Heyne et al. 2018 ??? We probe a potential architectural role for SMCHD1 and investigate the mechanism by which it shapes the Xi and represses gene expression --- ### <i class="fas fa-key" aria-hidden="true"></i><span class="visually-hidden">keypoints</span> Key points - --- ## Thank you! This material is the result of a collaborative work. Thanks to the [Galaxy Training Network](https://wiki.galaxyproject.org/Teach/GTN) and all the contributors!
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