- 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: 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.
Standard Bioinformatics Analysis
- Data filtering (removing adaptor sequences, contamination and low-quality reads from raw reads) and Production Statistics
- 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 (DGE data is required)
- UCSC Genome Browser instruction
Advanced Bioinformatics Analysis
- ChIP Sequencing Reads Distribution around TSS (Based on mRNA expression data, 1 and 2)
Custom Bioinformatics Analysis
- We can also perform customized analysis to meet requirements of specific projects.
For the ChIPed DNA samples you will 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 (the more the better) for every single library preparation.