ChIP-Seq analysıs
ChIP-Seq utilizes a combination of chromatin immunoprecipitation (ChIP) assays with high-throughput sequencing to study protein-chromatin interaction. By analyzing ChIP-Seq data, the interacting regions or binding sites of proteins such as transcription factors or histone marks can be detected across the genome. This will further allow the identification of genes that could be regulated by chromatin-associated proteins.
Case Study
We’re interested in the role of transcription factor, HNF4a, in liver tissues. Can we identify the chromatin regions bound by HNF4a?
A ChIP-Seq library will be created by pulling down samples with HNF4a antibody, and the ChIP-Seq data generated can be used to study the genome-wide binding profile of HNF4a. Binding sites of HNF4a can be visualized as peaks (Figure 1.1) and can be classified according to the types of regions that they are present in along the chromatin (Figure 1.2). If carried out together with histone ChIP-Seq data of the same tissues, we are also able to study the mechanisms of histone modification in regulating gene expression under different conditions such as in disease.
Figure 1.1: Binding profile of HNF4a and different histone marks along a region in Chromosome 10. Both binding and histone modification signal are indicated as peaks.
Figure 1.2: Classification of HNF4a binding sites in liver tissues.
Figure 1.3: Overall HNF4A binding profile and different histone modification signal at transcriptional start site (TSS) across the genome. Profile comparison of different phenotypes could give insight into the downstream genes which playing the regulation role.
Standard Analysis Workflow:
Standard Analysis Workflow:
- FREE initial consulation includes discussion on project objectives and result expectation, analysis method proposal, timeline and cost estimation.
- Standard data analysis includes primary sequencing reads quality control to downstream reads quatification and functional profiling for up to 12 samples. Please refer to analysis catalog for detail analysis workflow and result description.
- Publication ready figures/plots includes customize processing of analysis result plots such as spliting by samples group/conditions, color selection, highligting specific components within the plot etc. Only applies to analysis result of samples in package analysis.
- Publication submission consulation includes compilation of publication ready analysis result, scientific writing review, scientific plots review or customization, consultation for reviewer queries for up to 5 hours in total.
- Data integration includes intergration of existing pre-processed data for up to two applications between RNA-Seq, ChIP-Seq, or ATAC-Seq.
- TCGA differential expression and correlation analysis profiles various cancer types and identifies the most associated genes and pathways related to gene of interest. Please refer to our TCGA Analysis page for more information.
- Customize bioinformatic analysis: USD 370 / hour
- Standard data analysis: USD 110 / sample
- Bioinformatics consulation: USD 110 / hour
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