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  • Using the Human Protein Atlas – Tips and Tricks

    3 December 2016

    San Francisco, United States of America

    Using the Human Protein Atlas – Tips and Tricks Organizer: Tove Alm, KTH Royal Institute of Technology This practical workshop will give you knowledge on why and how to use the Human Protein Atlas database ( The Human Protein Atlas portal is a publicly available database with millions of high-resolution images showing the spatial distribution of proteins in normal human tissues, cancer tissues, and different human cell lines. Antibody-based methods have been used together with transcriptomic analysis to explore the human proteome. The data are publicly available and include application-specific validations for each antibody. During the workshop different areas of the Protein Atlas will be explored, with a focus on the new Cell Atlas launching Dec. 4, 2016. Practical questions will be handed out that are solved by hands-on use of the Human Protein Atlas. Presentations: 1:30-1:35 pm – Welcome. Tove Alm, KTH Royal Institute of Technology 1:35-1:55 pm – Introduction to the Human Protein Atlas. Mathias Uhlén, KTH Royal Institute of Technology 1:55-2:15 pm – Spatial localization of proteins in the Tissue Atlas. Cecilia Lindskog, Uppsala University 2:15-2:35 pm – All about the Pathology Atlas. Fredrik Pontén, Uppsala University 2:35-2:45 pm – Break 2:45-3:05 pm – High-resolution: The Cell Atlas. Emma Lundberg, KTH Royal Institute of Technology 3:05-3:25 pm – Antibody validation for bioimaging. Lars Björk, KTH Royal Institute of Technology 3:25-3:45 pm – Working with the downloadable Human Protein Atlas data. Kalle von Feilitzen, KTH Royal Institute of Technology 3:45-3:55 pm – Concluding remarks and future prespective. Mathias Uhlén, KTH Royal Institute of Technology 3:55-4:10 pm – Break 4:10-5:30 pm – Practical session with General Questions and Answers 2016-12-03 13:30:00 UTC 2016-12-03 17:30:00 UTC ASCB 2016 Moscone Center, San Francisco, United States of America Moscone Center San Francisco San Francisco County United States of America Protein databases Protein expression [] Tove Alm, KTH Royal Institute of Technology [] Life Science Researchers meetings_and_conferencesworkshops_and_courses [] protein family databasesImaging
  • Epigenomic Data Analysis

    15 - 16 June 2017

    Montreal, Canada

    Epigenomic Data Analysis High-throughput sequencing of Chromatin-Immunoprecipitated libraries (ChIP-seq) and of bisulfite converted DNA (WGBS) have become increasingly common and have largely supplanted microarrays for chromatin and DNA methylation profiling. When processed appropriately, ChIP-seq data provides base-pair resolution representations of transcription factor DNA-binding events and nucleosome (histone) modifications genome-wide. Similarly, WGBS can provide a quantitative genome wide profile of cytosine methylation. The CBW has developed a 2-day course providing an introduction to histone ChIP-seq and WGBS data analysis followed by integrated tutorials demonstrating the use of open source ChIP-Seq and WGBS analysis packages. The tutorials are designed as self-contained units that include example data and detailed instructions for installation of all required bioinformatics tools (FASTQC, BWA, MACS2, FindER, samtools, Picard, BisSNP). The course also includes an overview of integrative epigenomic tools that have been developed to explore ChIP-Seq and WGBS data together with other epigenomic datasets such as RNA-seq, DHS-seq and ATAC-seq. Participants will gain practical experience and skills to be able to: Align ChIP-seq and WGBS sequence data to a reference genome (required) Identify narrow and broad peaks from ChIP-seq data Identify methylated levels from WGBS data Visualize and summarize the output of ChIP-Seq and WGBS analyses Explore integrative tools for epigenomic data sets 2017-06-15 08:30:00 UTC 2017-06-16 17:00:00 UTC Montreal, Montreal, Canada Montreal Montreal Montreal Canada ChIP-seq Epigenomics [] [] [] 30 workshops_and_courses registration_of_interest []

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