Chromatin Immunoprecipitation and the Chip on Chip technique. Fredrik Fagerström Billai B E A- Core...

Chromatin Immunoprecipitation and the

Chip on Chip technique.

Fredrik Fagerström BillaiB E A- Core Facility forB E A- Core Facility for

BBioinformatics and ioinformatics and EExpression xpression AAnalysis.nalysis.Department of Biosciences & Nutrition Department of Biosciences & Nutrition

Karolinska InstitutetKarolinska Institutet

Agenda

-General introduction to Chromatin and Transcriptional and Epigenetic control.

-Chromatin Imunnoprecipitation, tiling arrays and the ”Chip on Chip” technique

Fredrik Fagerström Billai , BEA

Chromatin

A = 30nm fiber of an interphase chromosomeB = Nucleosomes along a strand of DNA

Images of Chromatin

The Chromatin Subunit model

The Nucleosome Crystal Structure

Histones are modified at Specific Amino Acids

Histone Code hypothesis - Modifications of the Histone tails act as marks that can be read by other proteins to control the expression or replication of chromosomal regions. The coding in the histones may

be heritable.

Specific modifications are associated with specific functions.

Transcriptional gene silencing

Chromatin compaction

Genome stability

X chromosome inactivation (females)

Methylation of DNA

Eukaryotic mRNAs are synthesized by the Pol II complex

Gene regulation in the eukaryotes

Wasserman and Sandelin (2004)

Chromatin Immunoprecipitation

Chip- General outline

Chip analysis of ERα recruitment to estrogen responsive gene promoters.

Ray et al. 2006

Chip Quantification

Calella et al. 2007

Real Time PCR quantification

Chip on Chip Outline

Genome Wide Chip Solutions

Affymetrix Tiling ArraysClassic Two Color Arrays Illumina Deep Sequencing

Millions of copies of a specificoligonucleotide probe

Single stranded, labeled ‘target’

Oligonucleotide ‘probe’

1.28cm

GeneChip Probe Array

1.28cm

Affymetrix array architecture

Affymetrix genechip familyAffymetrix genechip family

Tiling Arrays

Fredrik Fagerström Billai , BEABoyer et al. 2005

Tiling arrays provide high resolution for identifying bound fragments

Overlapping 25-mer fragments

Quantile Normalization

Identifying bound genomic fragments by Intensity Percentile Ranking.

Integrated Genome Browser, IGB

Genome-wide profiling of PRC1Polycomb chromatin binding in Drosophila melanogaster.

Chip profiles

Chromatin Immunoprecipitation and the Chip on Chip technique. Fredrik Fagerström Billai B E A- Core...

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Transcript of Chromatin Immunoprecipitation and the Chip on Chip technique. Fredrik Fagerström Billai B E A- Core...

IMMUNOTECHNIQUES (immunoprecipitation)

ChIP-IT® FFPE Chromatin Preparation IIOverview Chromatin Immunoprecipitation (ChIP) is a powerful tool for studying protein/DNA interactions, including transcription factors, co-regulatory

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High Sensitivity Chromatin Preparation - Active Motif · Technical Services..... 22. 1 Overview Chromatin Immunoprecipitation (ChIP) is a powerful tool for studying protein/DNA interactions,

Transcription ChIP kit - Diagenode€¦ · Transcription ChIP kit Transcription Chromatin Immunoprecipitation kit Cat. No. C01010090 (kch-redTBP-012) Instruction Manual Version 3

Measuring Protein-DNA interactions ... - DTU … · Measuring Protein-DNA interactions using Chromatin Immunoprecipitation and NGS (ChIP-Seq)

Guide to Chromatin Immunoprecipitation

Immunoprecipitation on Benchpaper

Immunoprecipitation (IP) - tools.thermofisher.comtools.thermofisher.com/content/sfs/brochures/TR0064-Immunoprecipitation-guide.pdf · Non-bound sample components are washed away,

Supplementary Materials and Methods. Chromatin ...morozov/pdfs/Zawadzki_Morozov_Broach_MBC200… · Supplementary Materials and Methods. Chromatin immunoprecipitation . ChIP was performed

Supporting Online Material for - Science · Supporting Online Material (SOM) Materials and Methods ChIP Seq.Chromatin immunoprecipitation for NFκB was carried out as previously described

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(hMeDIP) ChIP Kit Immunoprecipitation DNA ... · 11.DATA ASSAY ANALYSIS PROCEDURE 10 12.RESOURCES ANALYSIS 13 13. TROUBLESHOOTING 15 14. NOTES 18 ... immunoprecipitation of 5-hmC-enriched

Rachel Imoberdorf, PhD Senior Development Scientist · Chromatin Immunoprecipitation (ChIP) Allows quantitative analysis of Protein-DNA interactions in vivo. • Localisation of proteins

RNA-Binding Protein Immunoprecipitation

Chromatin Immunoprecipitation DNA Sequencing (ChIP-seq)

Chromatin, Gene, and RNA Regulation · Chromatin immunoprecipitation Chromatin immunoprecipitation (ChIP) analyses were conducted as described previously (23). The primers for quantitativereal-timePCR(qPCR)arelistedinSupplemen-tary

SLFN11 IsaTranscriptionalTargetofEWS-FLI1and … · the NCI Drug Developmental Therapeutics Program (DTP). Chromatin immunoprecipitation sequencing data analysis The ChIP-Seq dataset

SimpleChIP Enzymatic Chromatin IP Kit (Agarose Beads)media.cellsignal.com/pdf/9002.pdf106 cells per immunoprecipitation. This kit is not compatible with ChIP-Seq because the ChIP-Grade