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First archived on: 2016-04-25

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... library preparation ChIP Seq is the latest next generation sequencing method to analyze protein interactions with genomic DNA This technique enables genome wide profiling analysis of binding sites for any protein of interest and is important to understand transcriptional regulation mediated by transcription factors chromatin remodelers and histone variants In this workshop we will briefly review the bench protocol for ChIP Seq library preparation ChIP Seq data analysis In the workshop we will start with the raw FASTQ format files obtained from Illumina sequencers and go through mapping of the raw reads removal of duplicate reads generation of signal intensity files peak calling enrichment analysis and data visualization with Picower bioinformatics server We will use some publicly available ChIP Seq data for the demo Please note that the workshop will last for 1 hour and all the participants are recommended to bring their own laptops for hands on practice Speaker Fan Gao Ph D The Picower Institute for Learning and Memory at MIT Fan is a staff bioinformatician with PILM Before moving to MIT Fan was working as a research associate at University of Southern California with a joint appointment at Zilkha Neurogenetic Institute and Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research Additional Details Additional Details Organizer The Picower Institute for Learning and Memory Calendar GoogleCal 43 Vassar ST Room 46 3310 Cambridge MA 02139 27 Apr 4 00 pm 5 00 pm Aging Brain Initiative Seminar Series with Dr Morgan Sheng New mechanistic insights into Alzheimer s and other neurodegenerative diseases 4 00 pm 5 00 pm 43 Vassar ST Room 46 3310 Cambridge MA 02139 Event Type Aging Brain Seminar Series Availability Public Event Time Wednesday 4 00 pm 5 00 pm Location Room 46 3189 43 Vassar ST Room 46 3310 Cambridge MA 02139 Abstract Alzheimer s disease AD afflicts five million people in the US and millions more globally but its pathogenesis remains poorly understood at the molecular and cellular level Our approach is to start from human genetics Genetic variants in TREM2 Triggering Receptor Expressed on Myeloid cells 2 greatly increase the risk of Alzheimer s disease AD 3 fold increase in risk which is on par with the largest genetic risk factor for AD apolipoprotein E4 APOE4 TREM2 is specifically expressed in myeloid cells and only by microglia in the brain implicating innate immunity mechanisms in the pathogenesis of AD I will present evidence that links TREM2 biochemically and functionally with two other major AD risk genes APOE and APOJ which encode apolipoproteins By revealing the cell biological function of TREM2 in microglia our findings can explain why mutations in TREM2 increase beta amyloid accumulation and elevate the risk of AD Human genetics point towards a crucial role of autophagy in the etiology of another class of neurodegenerative diseases ALS FTD amyotrophic lateral sclerosis frontotemporal dementia Haploinsufficiency of Progranulin a secreted protein is a common genetic cause of FTD Our studies have revealed that Progranulin is unexpectedly involved in...

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