Schema for Agilent Array - Agilent Microarray Probesets
  Database: hg18    Primary Table: snpArrayAffy6    Row Count: 909,508   Data last updated: 2007-10-08
Format description: Affy 100K SNP array (HindIII)
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 589int(10) unsigned For browser speedup
chrom chr1varchar(255) Reference sequence chromosome or scaffold
chromStart 554483int(10) unsigned Start position in chrom
chromEnd 554484int(10) unsigned End position in chrom
name SNP_A-8575125varchar(255) Identifier
score 0int(10) unsigned Not used
strand +char(1) Strand: +, - or ?
observed C/Tblob Observed alleles
rsId rs10458597varchar(64) dbSNP identifier

Connected Tables and Joining Fields
        hg18.snp126.name (via snpArrayAffy6.rsId)
      hg18.snp126Exceptions.name (via snpArrayAffy6.rsId)
      hg18.snp126orthoPanTro2RheMac2.name (via snpArrayAffy6.rsId)
      hg18.snpArrayAffy250Nsp.rsId (via snpArrayAffy6.rsId)
      hg18.snpArrayAffy250Sty.rsId (via snpArrayAffy6.rsId)
      hg18.snpArrayAffy5.rsId (via snpArrayAffy6.rsId)
      hg18.snpArrayIllumina300.name (via snpArrayAffy6.rsId)
      hg18.snpArrayIllumina550.name (via snpArrayAffy6.rsId)
      hg18.snpArrayIllumina650.name (via snpArrayAffy6.rsId)
      hg18.snpSeq.acc (via snpArrayAffy6.rsId)

Sample Rows
 
binchromchromStartchromEndnamescorestrandobservedrsId
589chr1554483554484SNP_A-85751250+C/Trs10458597
589chr1554635554636SNP_A-85751150-A/Grs9629043
589chr1557615557616SNP_A-85753710-C/Trs11510103
590chr1711152711153SNP_A-87096460-C/Grs12565286
590chr1730719730720SNP_A-84977910-C/Trs12082473
590chr1742428742429SNP_A-19094440-C/Trs3094315
590chr1751594751595SNP_A-83580630+C/Trs2286139
590chr1755131755132SNP_A-83298920+A/Grs11240776
590chr1766984766985SNP_A-84089120+A/Trs2980319
590chr1775851775852SNP_A-18869330-A/Grs2980300

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

Agilent Array (genotypeArrays) Track Description
 

Description

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

Agilent's oligonucleotide aCGH platform facilitates genome-wide DNA copy number variation profiling without amplification or complexity reduction. Probe coverage spans both coding and non-coding regions, with emphasis on well-characterized genes, particularly cancer-relevant genes.

The track consists of the following subtracks:

SurePrint G3 CGH Microarray 1x1M AMADID 021529

This annotation displays the probe positions for the SurePrint G3 Human CGH 1 x 1M microarray from Agilent Technologies, Inc.
  • Over 963,000 coding and non-coding human sequences represented
  • 2.1 kb overall median probe spatial resolution
  • 1 x 1M slide format printed using Agilent's 60-mer SurePrint technology

SurePrint G3 High-Resolution Discovery Microarray 1x1M AMADID 023642

This annotation displays the probe positions for the SurePrint G3 Human Human High-Resolution Discovery 1 x 1M microarray from Agilent Technologies, Inc.
  • 963,000+ human sequences represented
  • 2.6 KB overall median probe spacing, 3 KB average probe spacing
  • 1 x 1M slide format printed using Agilent's 60-mer SurePrint technology
  • Unlike the catalog CGH and CNV microarrays, this array design is not a gene-biased or CNV-biased design.

SurePrint G3 CGH Microarray 2x400K AMADID 021850

This annotation displays the probe positions for the SurePrint G3 Human CGH 2 x 400K microarray from Agilent Technologies, Inc. This format has the flexibility to run two samples on a single chip.
  • Over 411,000 coding and non-coding human sequences represented
  • 5.3 kb overall median probe spatial resolution
  • 2 x 400K slide format printed using Agilent's 60-mer SurePrint technology

SurePrint G3 CGH Microarray 4x180K AMADID 022060

This annotation displays the probe positions for the SurePrint G3 Human CGH 4 x 180K microarray from Agilent Technologies, Inc. This format has the flexibility to run four samples on a single chip.
  • Over 170,000 coding and non-coding human sequences represented
  • 13 kb overall median probe spatial resolution
  • 4 x 180K slide format printed using Agilent's 60-mer SurePrint technology

SurePrint G3 CGH Microarray 8x60K AMADID 021924

This annotation displays the probe positions for the SurePrint G3 Human CGH 8 x 60K microarray from Agilent Technologies, Inc. This format has the flexibility to run eight samples on a single chip.
  • Over 55,000 coding and non-coding human sequences represented
  • 41.4 kb overall median probe spatial resolution
  • 8x60K slide format printed using Agilent's 60-mer SurePrint technology

CGH Microarray 1x244k AMADID 014693

This annotation displays the probe positions for the Human Genome CGH 1 x 244K microarray from Agilent Technologies, Inc.
  • Over 236,000 coding and non-coding human sequences represented
  • 8.9 kb overall median probe spatial resolution (7.4 kb median probe spacing in Refseq genes)
  • 1 x 244K slide format

CGH Microarray 2x105k AMADID 014698

This annotation displays the probe positions for the Human Genome CGH 2 x 105K microarray from Agilent Technologies, Inc.
  • Over 99,000 coding and non-coding human sequences represented
  • 21.7 kb overall median probe spatial resolution (18.9 kb median probe spacing in Refseq genes)
  • 2 x 105K slide format

CGH Microarray 4x44k AMADID 014950

This annotation displays the probe positions for the Human Genome CGH 4 x 44K microarray from Agilent Technologies, Inc.
  • Over 42,000 coding and non-coding human sequences represented
  • 43 kb overall median probe spatial resolution (24.2 kb median probe spacing in Refseq genes)
  • 4 x 44K slide format

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. PNAS. 2004 Dec 21;101(51):17765-70.

Credits

Thanks to Shane Giles, Peter Webb, and Dione Bailey from Agilent Technologies for providing these data.