Schema for Illumina WG-6 - Alignments of Illumina WG-6 3.0 Probe Set
  Database: hg18    Primary Table: illuminaProbes    Row Count: 44,163   Data last updated: 2008-06-12
Format description: Browser extensible data
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 4404int(10) unsigned range Start position in chromosome
chromEnd 4454int(10) unsigned range End position in chromosome
name ILMN_1761068varchar(255) values Name of item
score 1000int(10) unsigned range Optional score, nominal range 0-1000
strand -char(1) values + or -
thickStart 4404int(10) unsigned range Start of where display should be thick (start codon)
thickEnd 4454int(10) unsigned range End of where display should be thick (stop codon)
reserved 1int(10) unsigned range Used as itemRgb as of 2004-11-22
blockCount 1int(10) unsigned range Number of blocks
blockSizes 50,longblob   Comma separated list of block sizes
chromStarts 0,longblob   Start positions relative to chromStart

Connected Tables and Joining Fields
        hg18.illuminaProbesAlign.qName (via illuminaProbes.name)
      hg18.illuminaProbesSeq.id (via illuminaProbes.name)

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStarts
585chr144044454ILMN_17610681000-440444541150,0,
585chr145594609ILMN_17391991000-455946091150,0,
585chr184218471ILMN_17236571000-842184711150,0,
585chr11441614466ILMN_17498321000-14416144661150,0,
585chr15933859388ILMN_17766011000+59338593881150,0,
585chr15951159561ILMN_22007381000+59511595611150,0,
585chr1118864118917ILMN_17053261000-1188641189171211,39,0,14,
585chr1130072130122ILMN_16981641000-1300721301221150,0,
586chr1150546151220ILMN_18574131000-150546151220137,13,30,0,630,644,
586chr1157863157913ILMN_16669351000-1578631579131150,0,

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

Illumina WG-6 (illuminaProbes) Track Description
 

Description

This track displays the probes from the Illumina WG-6 3.0 BeadChip. The WG-6 BeadChip contains probes for the following set of RNA transcripts:

Probe sourceNumber of probes Number of unique probe sources
RefSeq NM (well-established coding transcript)27,454 22,435
RefSeq XM (provisional coding transcript)7,870 7,518
RefSeq NR (well-established non-coding transcript)446 358
RefSeq XR (provisional non-coding transcript)196 190
UniGene ESTs12,83712,837
TOTAL48,80343,338

Display

The track shows the location of the probes on the genome after the RNAs they correspond to were all aligned to the genome using BLAT. Alignment scores range from 0 to 1000, where 1000 is a perfect score. In the display, darker browns are for higher-scoring alignments.

Click on a probe track item to see detailed information about that probe ID. View the base-by-base alignment for that probe by clicking the "View Alignment" link on the details page.

Methods

The probe set was collected from the NCBI GEO (Gene Expression Omnibus), and the 43,338 RNA sequences were collected from Genbank using NCBI's EUtils interface to Entrez. These RNAs were aligned to the genome using BLAT, and 43,224 of them aligned well to 46,432 locations on the genome. The single best alignment was used, except in 1,789 cases where the RNA mapped equally well to two or more locations. The probes were then aligned to their respective RNAs using BLAT, and if a good alignment resulted, the probe was then mapped through to the genome using the combination of the probe-on-RNA and the RNA-on-genome alignments. Of the 48,803 original probes, 40,852 map well through this procedure to 44,163 locations on the genome.