- 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
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).
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, supporting the value of exploring similarly complex genomes in future research.
10 roots and shoots from 10 seedlings of B73
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.
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
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.
For the ChIPed DNA samples you need provide:
- Purity: OD260/280=1.8-2.0
- Concentration: ≥1ng/μl.
- Basic Requirements:
- 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.
- 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.