Schema for Array Probesets - Microarray Probesets
  Database: hg38    Primary Table: genetiSureCytoCghSnp8x60 Data last updated: 2022-05-26
Big Bed File Download: /gbdb/hg38/snpCnvArrays/agilent/hg38.GenetiSure_Cyto_CGH_Microarray_8x60K_085590_D_BED_20200302.bb
Item Count: 57,440
The data is stored in the binary BigBed format.

Format description: Browser Extensible Data
fieldexampledescription
chromchr1Reference sequence chromosome or scaffold
chromStart166017880Start position in chromosome
chromEnd166017940End position in chromosome
nameA_18_P10365585Name of item.

Sample Rows
 
chromchromStartchromEndname
chr1166017880166017940A_18_P10365585
chr1166067329166067389A_18_P10365809
chr1166157286166157346A_18_P10361476
chr1166296004166296064A_16_P15328538
chr1166355809166355868A_16_P15328660
chr1166452756166452816A_16_P15328847
chr1166514968166515028A_16_P56227263
chr1166563266166563326A_16_P15329017
chr1166626126166626186A_16_P15329171
chr1166694731166694791A_16_P00184234

Array Probesets (genotypeArrays) Track Description
 

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.

Affymetrix Cytoscan HD GeneChip Array

The CytoScan HD Array, which is included in the CytoScan HD Suite, provides the broadest coverage and highest performance for detecting chromosomal aberrations. CytoScan HD Suite has greater than 99% sensitivity and can reliably detect 25-50kb copy number changes across the genome at high specificity with single-nucleotide polymorphism (SNP) allelic corroboration. With more than 2.6 million copy number markers, CytoScan HD Suite covers all OMIM and RefSeq genes.

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.

The Affymetrix Cytoscan HD GeneChip Array track was created by converting the CytoScanHD_Accel_Array.na36.bed.zip 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.