Schema for Agilent CGH - Agilent CGH Microarray probesets
  Database: rn4    Primary Table: agilentCgh4x180k    Row Count: 174,012   Data last updated: 2010-09-01
Format description: Browser extensible data
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 22175int(10) unsigned range Start position in chromosome
chromEnd 22235int(10) unsigned range End position in chromosome
name A_86_P10000112varchar(255) values Name of item

Connected Tables and Joining Fields
        rn4.agilentCgh105a.name (via agilentCgh4x180k.name)
      rn4.agilentCgh1x1m.name (via agilentCgh4x180k.name)
      rn4.agilentCgh244a.name (via agilentCgh4x180k.name)

Sample Rows
 
binchromchromStartchromEndname
585chr12217522235A_86_P10000112
585chr1110045110105A_86_P10000223
586chr1197078197138A_86_P10000585
586chr1242176242236A_86_P10000758
586chr1260038260098A_86_P10000848
587chr1279202279262A_86_P10000913
587chr1310526310586A_86_P10001010
587chr1326287326347A_86_P10001126
587chr1358003358063A_86_P10001269
587chr1371197371257A_86_P10001278

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Agilent CGH (genotypeArrays) Track Description
 

Description

This track displays the probes from the Agilent Catalog Oligonucleotide Microarrays.

Agilent's oligonucleotide CGH (Comparative Genomic Hybridization) platform enables the study of genome-wide DNA copy number changes at a high resolution. The probes on Agilent aCGH 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.

The Agilent catalog CGH microarrays are printed on 1 in. x 3 in. glass slides and are available in several formats. The rat catalog SurePrint G3 microarrays formats are the 1x1M and 4x180K. The legacy rat catalog SurePrint HD microarrays are the 1x244K and 2x105K.

Subtracks were colored in alternating shades of green and orange to highlight track boundaries. The track consists of the following subtracks:

Description AMADID Samples per Slide Biological Features Median Probe Spacing Gene-biased
SurePrint G3 Rat CGH Microarray 1x1M 027065 1 966,967 1.7 kb Yes
SurePrint G3 Rat CGH Microarray 4x180K 027064 4 174,012 11 kb Yes
SurePrint HD Rat CGH Microarray 1x244K 015223 1 235,974 4.9 kb Yes
SurePrint HD Rat CGH Microarray 2x105K 015235 2 97,973 19 kb Yes

References

More information on the Agilent Oligonucleotide Microarrays is available here.

Barrett MT, Scheffer A, Ben-Dor A, Sampas N, Lipson D, Kincaid R, Tsang P, Curry B, Baird K, Meltzer PS et al. Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proc Natl Acad Sci U S A. 2004 Dec 21;101(51):17765-70. PMID: 15591353; PMC: PMC535426

Credits

Thanks to Shane Giles, Peter Webb, and Anniek De Witte from Agilent Technologies for providing these data.