chip-seq data identifying transcription factor binding ... · did my chip-seq worked?--...
TRANSCRIPT
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Identifying Transcription Factor Binding Sites from ChIP-seq Data
Reetu TutejaScience Analyst, CyVerse
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Learning objectives
Understand the nature of ChIP-seq data
Efficiently manage and analyze ChIP-seq data: from reads to peaks
How to do quality assessment using R ChIPQC package
Using CyVerse Discovery Environment apps to do ChIP-seq analysis
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What is ChIP-seq?
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How do cells know what to do?
Image source: cK12.org
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Transcriptional regulation
Wasserman et al, Nature Reviews 2004
Transcription factors are proteins that can activate or repress the expression of target genes through the binding on DNA cis-regulatory elements
Chromatin accessibility and histonemodification also regulate geneexpression
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Key steps in ChIP assay
ChIP DNA Input DNA
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Chipseq workflow: from reads to peaks
Did my ChIP-seq worked?-- Cross-Correlation score-- FRiP score
• MACS2 (Model-based analysis of ChIP-seq)
1. Pre-alignment processing • Removal of adapter sequences• Remove low-quality • Discard short-reads
2. Alignment Use any standard short-read alignment program
3. Peak Calling MACS2 (Model-based analysis of ChIP-seq)
4. Post-alignment processing
Tutorial Link: https://cyverse-chipseq-tutorial.readthedocs-hosted.com/en/latest/index.html
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Downstream analyses
Park et al, Nature Reviews 2009
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ChIP signal
Jothi et al (2008) Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data
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ChIP signal vs artifact signal
Landt et al (2012) ChIP-seq guidelines and practices for the ENCODE and modENCODE consortia
Plus strandMinus strand
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Cross-correlation score
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Successful vs failed ChIP
Strand shift (bp) Strand shift (bp) Strand shift (bp)
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CyVerse is supported by the National Science Foundation under Grants No. DBI-0735191, DBI-1265383 and DBI-1743442.