PLoS Genetics

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First surprise: Input DNA has structure Input DNA profile shows peaks itself and is not “flat” The Pol2 antibody is exceptional. For ChIP with a “typical” antibody, the input DNA peaks could affect the ability to call significant peaks 8
Origin of Input DNA from Nuclear Lysate 1. Reverse cross-links 2. Phenol-chloroform extract 3. Purify DNA 4. Size select DNA 5. Ligate Illumina adapters What happens if we change some of these variables 9
Page 1 and 2: Elucidating Transcriptional Regulat
Page 3 and 4: g DNA folding Transcriptional Regul
Page 5 and 6: ChIP-Seq 5
Page 7: Highlights from Key Papers Nature B
Page 11 and 12: Reference Types We Examined Input D
Page 13 and 14: Aggregation Plot Expressed Genes (T
Page 15 and 16: Regions Associated with Transcripti
Page 17 and 18: Summary and Bioinformatics Contribu
Page 19 and 20: Considerations with Early Peak Call
Page 21 and 22: Chromatin Remodeling: Why You Shoul
Page 23 and 24: Role in Cancer SWI/SNF subunit Canc
Page 25 and 26: Project Overview Analysis Questions
Page 27 and 28: How to Combine Data 27
Page 29 and 30: SWI/SNF Co-occurrences CTCF, Pol II
Page 31 and 32: Pathway Analysis Euskirchen and Aue
Page 33 and 34: Summary and Bioinformatics Contribu
Page 35 and 36: Exploring Transcription, DNA Foldin
Page 37 and 38: So How Does ChIA-PET Work (Cliffs N
Page 39 and 40: The Textbook Version 39
Page 41 and 42: Second Goal - Formation of Protein
Page 43 and 44: Gene Expression Characteristics Li,
Page 45 and 46: IRS1 and T2D: Long Range Interactio
Page 47 and 48: Bioinformatics Contributions Integr
Page 49 and 50: Combining RNAPII ChIP-Seq with RNA-
Page 51 and 52: CAPE: Coupled Analysis of Polymeras
Page 53 and 54: Sample CAPE-compare Output (raw) 53
Page 55 and 56: Sample CAPE-compare Output (Venn) 5
Page 57 and 58: Other Work While at Yale Co-author
Page 59:
Questions 59
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