This genomic 15K CGH array was custom designed against zebrafish (Danio rerio) genome assembly danRef5/Zv7 (available at: http://hgdownload.cse.ucsc.edu/goldenPath/danRer5/bigZips/) on the basis of a database of seven million genomic probe sequences provided by Agilent. Probe sequences were later re-mapped with respect to genome assembly danRer6/Zv8 (http://hgdownload.cse.ucsc.edu/goldenPath/danRer6/bigZips/). During this process, probes were annotated with respect to the quality of their mapping to the Zv8 assembly - see table columns 'Zv8:ProbeRemapped' and 'Zv8:ProbeRemappedQualityCode'. The quality code is defined as follows: Primary code: A: Perfect match over entire probe sequence B: Probe sequence matches contiguously with 1 mismatch (BLAT blockCount=1) C: Probe sequence matches contiguously with 2-5 mismatches (BLAT blockCount=1) X: No match for probe sequence in genomic (Zv8) BLAT results => probe not used under Zv8. Z: Best BLAT match worse than per code C => probe not used under Zv8 Primary code qualifiers (suffixes): ' = duplicate matches (quality A,B,C) within under 50K ^ = duplicate matches (quality A,B,C) within 50K-250K (Longer intervals than 250K between duplicate matches led to rejection => primary code Z) + = several matches (4-10), regardless of location and quality # = many matches (>10), regardless of location and quality
Highly Aneuploid Zebrafish Malignant Peripheral Nerve Sheath Tumors have Genetic Alterations Similar to Human Cancers
Data table header descriptions
ID
ProbeName
Probe identifier, alphanumeric (provided by Agilent)
Row
Probe row on microarray (provided by Agilent)
Col
Probe column on microarray (provided by Agilent)
SubTypeMask
Numeric code defining the subtype of any control feature (provided by Agilent)
ControlType
Control type of probe. 1=positive, -1=negative, 0=none (provided by Agilent)
ProbeUID
Unique integer for each unique probe in a design (provided by Agilent)
ProbeLength
Probe length
SEQUENCE
Probe sequence
Zv7:Chr
Chromosomal location for probe in Zv7 genome assembly
Zv7:PStart
Start position of probe sequence in Zv7 genome assembly
Zv7:PEnd
End position of probe sequence in Zv7 genome assembly
Zv7:Strand
Strand of probe sequence in Zv7 genome assembly
Zv8:Chr
Chromosomal location for probe in Zv8 genome assembly
Zv8:PStart
Start position of probe sequence in Zv8 genome assembly
Zv8:PEnd
End position of probe sequence in Zv8 genome assembly
Zv8:Strand
Strand of probe sequence in Zv8 genome assembly
Zv8:ProbeSpan
Genomic range encompassed by probe match(es) in Zv8 assembly. Not equal to probe length for double matches in close vicinity, see Zv8:ProbeRemappedQualityCode!
Zv8:ProbeRemapped
Remap status of probe in Zv8 assembly. 1=remapped, 0=not remapped
Zv8:ProbeRemappedQualityCode
Code for probe remap quality from Zv7 to Zv8. Codes: see Description
Less...
More...