CD BioSciences helps clients obtain plant genome-wide information on the interactions of specific DNAs with target proteins through the combination of chromatin immunoprecipitation (ChIP) and high-throughput sequencing.

The Introduction of ChIP-Seq

ChIP-seq service is to obtain high-quality reads based on library sequencing of qualified DNA samples from IP downstream and to determine the specificity of IP experiments by motif. It can efficiently predict relevant genes and analyze their functional enrichment. Predict the function of specific proteins, histone chromosome binding profiles, and epigenetic modifications of DNA.

Service Content

Experimental content

• DNA and protein cross-linking.
• Cell lysis to extract nuclear DNA.
• Chromosome fragmentation processing.
• Immunoprecipitation to obtain antibody target protein DNA complex.
• DNA cross-linking and purification.
• Library sequencing and data analysis, including library construction, library quality inspection, sequencing, and information analysis.

Data analysis

The type of ChIP-seq we provide

• Crosslinking/X-ChIP

We provide Crosslinking/X-ChIP which is the mainstream solution of CHIP-seq. Formaldehyde crosslinking is used to immobilize DNA to protein binding, which binds solidly and allows for the study of transcription factor binding but may be epitope masked.

• Native/N-ChIP

We use micrococcal nuclease (MNase) cleavage of chromatin to obtain DNA fragments. Native/N-ChIP is generally used to research histone modifications and is an alternative when X-CHIP epitope masking is severe.

Sample Requirements and Preparation

Sample types include DNA samples, cells, or tissue.

ChIPed DNA >10ng, cell >10⁷, or tissue >2g.

DNA fragments are 100-500bp in size with a clear major band. A gel map of the interrupted DNA is required.

ChIP standard antibodies, including H3K4Me3, H3K4Me2, H3K9Me3, H3K9Me2, H3K27Me3, H3K27Me , etc.

Recommended data volume 20M~40M clean reads.

Deliverables

1. Unprocessed original FASTQ file
2. Report with basic sequencing quality statistics
3. Mapping BAM files
4. Wiggle and BigWig tracks
5. ChIP-Seq quality measurements
6. Output files generated by data analysis software
7. Peak annotations

Technology Advantages

• High-quality and resolution sequencing can obtain millions of sequence tags and rare protein binding sites in the genome.
• Cost-effective, rapid genome-wide analysis of multiple samples at once.
• Micro-build libraries require only 5ng of DNA after immunoprecipitation.
• Flexible protocols choose the appropriate specific antibody according to project needs.

CD BioSciences has deep expertise in plant biology and molecular technology. We provide ChIP-seq projects including high-quality sequencing and comprehensive bioinformatics analysis, enabling genome-wide analysis of protein-DNA interactions in plants with high resolution and sensitivity. Please feel free to contact us if you have any other requests or questions.

For research use only, not for clinical use.