ChIP-Seq
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ChIP-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:

  1. Wide detection range: Genome wide protein DNA interaction studies
  2. Cost-effective: Less data required for identifying the binding sites in whole genome
  3. Only require low amount of ChIP DNA: More than 10ng ChIP-ed DNA is adequate

Genome-wide and Organ Specific Landscpaes of Epigenetic Modifications and Their Relationships to mRNA and smRNA Transcriptomes in Maize. Plant Cell 2009.21(4):1-53-1069.

This 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, opening the door to exploring similarly complex genomes in the future.

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Bioinformatics:

Standard Bioinformatics Analysis

  1. Data filtering (removing adaptor sequences, contamination and low-quality reads from raw reads) and Production Statistics
  2. Reads Alignment
  3. Genome-wide distribution of ChIP sequencing reads
  4. Genome-wide peak scanning and distribution
  5. GO function analysis of peak-related genes
  6. Difference analysis of multi-samples
  7. Tag detection near Transcription Start Sites (DGE data is required)
  8. UCSC Genome Browser instruction

Advanced Bioinformatics Analysis

  1. ChIP Sequencing Reads Distribution around TSS (Based on mRNA expression data, 1 and 2)

Custom Bioinformatics Analysis

  1. We can also perform customized analysis to meet requirements of specific projects.

Sample Requirements:

For the ChIPed DNA samples you will provide:

  1. Purity: OD260/280=1.8-2.0
  2. Concentration: ≥1ng/μl.
  3. 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 (the more the better) for every single library preparation.

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