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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](/training-material/topics/introduction) - [Sequence analysis](/training-material/topics/sequence-analysis) - Quality Control: [
slides](/training-material/topics/sequence-analysis/tutorials/quality-control/slides.html) - [
hands-on](/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.html) - Mapping: [
slides](/training-material/topics/sequence-analysis/tutorials/mapping/slides.html) - [
hands-on](/training-material/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 --- ### <i class="fa fa-question-circle" aria-hidden="true"></i><span class="visually-hidden">question</span> Questions - What is ChIP-seq? --- ### <i class="fa 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="fa 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!