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ChIP-Seq

Overview

ChIP-Seq

Chip-SeqChIP-Seq, also known as ChIP-Sequencing, is widely used to analyze protein interactions with DNA. It combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify binding sites of DNA-associated proteins, and can be used to precisely map global binding sites for any protein of interest. ChIP sequencing offers higher resolution and more precise and abundant information in comparison with array-based ChIP-chip.

Benefits:

  • Wide detection range: Genome wide protein DNA interaction studies
  • Cost-effective: Less data required for identifying the binding sites in whole genome
  • Only require low amount of ChIP DNA: As low as 5ng ChIP-ed DNA is adequate
Technical Information

Bioinformatics:

Standard Bioinformatics Analysis

  • Data filtering (removing adaptor sequences, contamination and low-quality reads from raw reads)
  • Reads Alignment
  • Genome-wide distribution of ChIP sequencing reads
  • Genome-wide peak scanning and distribution
  • GO function analysis of peak-related genes
  • Difference analysis of multi-samples
  • Tag detection near transcription start sites
  • UCSC Genome Browser instruction

Advanced Bioinformatics Analysis

  • ChIP sequencing reads distribution around transcription start sites

Custom Bioinformatics Analysis

  • We can also perform customized analysis to meet specific needs of your projects.

Sample Requirements:

For the ChIPed DNA samples you need provide:

  • Purity: OD260/280=1.8-2.0
  • Concentration: ≥1ng/μl.
  • Basic Requirements:
    1. Gel electrophoresis analysis result should be provided to make sure that the size of DNA fragments is between 100bp to 500bp, and most of the fragments should be about 250bp.
    2. DNA total amount ≥10ng (although 5ng is acceptable, the greater the amount, the better) for every single library preparation.

For the cell line samples you need provide:

  • Cell numbers (for single round of ChIP enrichment): 5×107 cells for the species whose genome size is similar to human.
  • Antibodies for ChIP enrichment:H3K4Me3, H3K4Me2, H3K9Me3, H3K9Me2,H3K27Me3, H3K27Me2, and other necessary antibodies are acceptable after evaluation.

Cases

Genome-wide and Organ Specific Landscpaes of Epigenetic Modifications and Their Relationships to mRNA and smRNA Transcriptomes in Maize. Plant Cell. 21(4):1-53-1069 (2009).

ChIP-Seq_1This study generated an integrated, genome-wide and organ-specific survey of epigenetic markers together with transcriptional outputs. The results demonstrate that Illumina/Solexa 1G sequencing and read mapping are feasible with high accuracy even in large and repeat-rich plant genomes, supporting the value of exploring similarly complex genomes in future research.

Samples:

10 roots and shoots from 10 seedlings of B73

Methods: 

Use ChIP-Seq, RNA-Seq, small RNA-Seq, and McrBC-Seq to perform genome-wide analysis of DNA methylation, histone modifications, sRNA, and mRNA transcriptional activity.

Results:

  1.  Transcriptional activity is associated with the ratio of H3K4me3 /H3K4me2
  2.  Two new types of siRNA were discovered
  3.  Three histone modifications,H3K4me3, H3K9ac, H3K36me3 were associated with transcriptional active genes

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