PLoS Genetics

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SWI/SNF Has 288 Subunit Combinations! ARID (1a or 1b or 2) * * * * 24
Project Overview Analysis Questions Where does SWI/SNF bind and in what configurations What other elements are associated with SWI/SNF binding sites Functional implications (pathway analysis, etc.) Experimental Procedure ChIP-Seq against Brg1, BAF155, BAF170, and Ini1 in HeLa S3 cells Mass spectrometry to inventory co-immunoprecipitating proteins 25
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 and 8: Highlights from Key Papers Nature B
Page 9 and 10: Origin of Input DNA from Nuclear Ly
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: Role in Cancer SWI/SNF subunit Canc
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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