Array Probesets Track Settings
 
Microarray Probesets   (All Variation tracks)

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 Agilent GenetiSure Cyto CGH+SNP  Agilent GenetiSure Cyto CGH+SNP 4x180K 085591 20200302   Schema 
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 Agilent GenetiSure Cyto CGH 4x180K  Agilent GenetiSure Cyto CGH 4x180K 085589 20200302   Schema 
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 Agilent GenetiSure Cyto CGH 8x60  Agilent GenetiSure Cyto CGH 8x60K 085590 20200302   Schema 
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 Illumina 450k  Illumina 450k Methylation Array   Schema 
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 Illumina 850k  Illumina 850k EPIC Methylation Array   Schema 
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 CytoSNP 850k  Illumina 850k CytoSNP Array   Schema 
    


updated Note: Aug. 31, 2022

Description

Agilent Arrays

The arrays listed in this track are probes from the Agilent Catalog Oligonucleotide Microarrays.

Please note that more microarray tracks are available on the hg19 genome assembly. To view those tracks, please click this link for hg19 microarrays. Microarrays that are not listed can be added as Custom Tracks with data from the companies.

Agilent GenetiSure Cyto

Agilent's oligonucleotide CGH (Comparative Genomic Hybridization) platform enables the study of genome-wide DNA copy number changes at a high resolution. The CGH probes on Agilent CGH microarrays are 60-mer oligonucleotides synthesized in situ using Agilent's inkjet SurePrint technology. The probes represented on the Agilent CGH microarrays have been selected using algorithms developed specifically for the CGH application, assuring optimal performance of these probes in detecting DNA copy number changes.

Illumina 450k and 850k Methylation Arrays

With the Infinium MethylationEPIC BeadChip Kit, researchers can interrogate over 850,000 methylation sites quantitatively across the genome at single-nucleotide resolution. Multiple samples, including FFPE, can be analyzed in parallel to deliver high-throughput power while minimizing the cost per sample. These tracks show positions being measured on the Illumina 450k and 850k (EPIC) microarray tracks. More information about the arrays can be found on the Infinium MethylationEPIC Kit website.

Illumina CytoSNP 850K Probe Array

The Infinium CytoSNP-850K v1.2 BeadChip provides comprehensive coverage of cytogenetically relevant genes on a proven platform, helping researchers find valuable information that may be missed by other technologies. It contains approximately 850,000 empirically selected single nucleotide polymorphisms (SNPs) spanning the entire genome with enriched coverage for 3,262 genes of known cytogenetics relevance in both constitutional and cancer applications.

Display Conventions and Configuration

Items in this track are colored according to their strand orientation. Blue indicates alignment to the negative strand, and red indicates alignment to the positive strand.

Methods

The Agilent arrays were downloaded from their Agilent SureDesign website tool on March 2022.

The Illumina 450k and 850k (EPIC) tracks were created using a few columns from the Infinium MethylationEPIC v1.0 B5 Manifest File (CSV Format) and was then converted into a bigBed.

The Illumina CytoSNP-850K track was created by downloading the CytoSNP-850K v1.2 Manifest File (CSV Format) (GRCh38) file and then converted into a bigBed file.

Data Access

The raw data can be explored interactively with the Table Browser or the Data Integrator. For automated analysis, the data may be queried from our REST API or downloaded from our Downloads site. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.

Credits

Thanks to the Aliglent and Illumina support teams for sharing the data and the UCSC Genome Browser engineers for configuring the data.