NimbleGen CGH analysis identifies genomic insertions and deletions and copy number changes at ultra-high resolution, genome wide or focused fine tiling, with high-definition CGH.

CGH microarray service consists of the following steps:

• Customer selects catalog array design, or works with Roche NimbleGen bioinformatics scientists to design a custom array. Customers purchase catalog arrays or custom arrays from NimbleGen.
• Customer supplies purified, undegraded sample and reference genomic DNA (Keck can provide a male or female gDNA reference sample if no reference is provided by the customer). For optimal labeling and hybridization effisiency, use of high quality DNA is requered. Please follow our instructions for sample submission. 

	385K arrays	HD2 arrays
Sample Required	2.5μg	6.5μg
Sample Concentration	>0.2μg/μl	>0.2μg/μl

• Keck labels the sample, performs the CGH hybridization, scans the array, extracts the data, and performs the segmentation analysis.

Chip-chip analysis maps regulatory protein binding sites genome wide for transcription factors, polymerases and histones, or target promoter regions with ChIP-chip analysis.

ChIP-chip microarray service consists of the following steps:

• Customer selects catalog array design, or works with Roche NimbleGen bioinformatics scientists to design a custom array. Customers purchase catalog arrays or custom arrays from NimbleGen.
• The customer prepares his or her samples, including immunoprecipitation and amplification, according to recommended protocols and ships these samples to NimbleGen. For recommended sample prep protocols, see www.chiponchip.org or the UC Davis Genome Center.

	385K arrays	HD2 arrays
Sample Required	4μg each IP and control samples	6.5μg each IP and control samples
Sample Concentration	>200 ng / μl	>200 ng / μl

• NimbleGen labels the samples, performs the hybridization, scans the array, extracts the data, and performs a preliminary data analysis.
• The customer receives the raw data, scaled log2-ratio data, peak data, promoter reports mapping peaks to genes, genome annotation.

Methylation analysis finds methylated regions genome-wide or within targeted promoters or CpG islands with NimbleGen's high-resolution DNA methylation analysis technology.

DNA methylation microarray service consists of the following steps:

• Customer selects catalog array design, or works with Roche NimbleGen bioinformatics scientists to design a custom array. Customers purchase catalog arrays or custom arrays from NimbleGen.
• Customer prepares samples, including immunoprecipitation with anti-5-methyl-cytidine (MeDIP, recommended) or the MBD protein method. The DNA is amplified (if required) according to recommended protocols. DNA needs to be 200 bp or greater in size.

	385K arrays	HD2 arrays
Sample Required	4μg each IP and control samples	6.5μg each IP and control samples
Sample Concentration	250-500 ng / μl	250-500 ng / μl

• Keck labels the samples, performs the hybridization, scans the array, extracts the data, and performs a preliminary data analysis.
• The customer receives the raw data, scaled log2-ratio data, p-value data, peaks data (methylated regions), genome annotation, reports listing peaks with associated transcripts and gene annotation information.