ChIP-chip combines Chromatin Immunoprecipitation (ChIP) with microarray to analyze how regulatory proteins interact with the genome and provide insight into the mechanisms for histone modification or gene regulation by transcription factors. Arraystar has designed a line of RefSeq and ncRNA promoter arrays to investigate epigenetic modifications and transcription factor binding sites in the promoter regions of mRNAs, lncRNAs and microRNAs.
Arraystar Epigenetic Arrays
|Arraystar Human RefSeq Promoter Array
||23,148 RefSeq promoters (-1,300 bp ~ 500 bp of TSS)
|Arraystar Mouse RefSeq Promoter Array
||22,327 RefSeq promoters (-1,300 bp ~ 500 bp of TSS)
|Arraystar Rat RefSeq Promoter Array
||15,987RefSeq promoters (-1,300 bp ~ 500 bp of TSS)
|Arraystar Human ncRNA Promoter Array
||27,248 lncRNA promoters (-1,300 bp ~ 500 bp of TSS)
|Arraystar Mouse ncRNA Promoter Array
||18,552 lncRNA promoters (-1,300 bp ~ 500 bp of TSS)
|Arraystar Human Cancer DMR Array
||12,113 DMRs and nearby 11,380 CpG islands and shores
|Arraystar Human Cancer Block Array
||7,088 blocks containing 2,554 mRNA, 8,481 lncRNA and 463 miRNA genes
Arraystar's specially-designed promoter microarrays are available only through our ChIP-chip service. We provide full-service, from sample preparation to in-depth data analysis. Just send us your samples, and we'll do the rest!
Please refer to Sample Submission for details in how to get your project started.
Customer to provide: Chromatin immunoprecipitated DNA enriched by specific antibodies
Arraystar to provide:
• Quality assessment of ChIP
• Linear amplification using SIGMA WGA kit
• Target preparation by labeling with Cy3/5
• Array hybridization, washing, and scanning
• Data extraction, analysis and summarization
Arraystar's bioinformatics team has extensive experience in analyzing ChIP-chip data. We provide our customers with thorough, comprehensive data analysis.
• Raw data extraction and data quality assessment
• Scaled log2 ratio of ChIP/input co-hybridized channel intensities; normalization with median-centering, quantile normalization, and linear smoothing
• Enrichment peak (EP) finding; peak description of location, length, peak score, and significance
• Peak annotation with mapped genomic features
• Track files for genome browser viewing
• Differential Enrichment Peak (DEP) analysis
• Summary Report
Figure 1. Annotation of ChIP enrichment peaks.
Figure 2. Genome browser view of a ChIP enrichment peak (red) bound to the IGSF3 gene promoter region. The microarray tiling probes are shown in blue.