The array was assembled using amplicons representing approximately 93% of the genes predicted in version 1.0 of the Drosophila genome from sequences released by the Berkeley Drosophila Genome Project and Celera Genomics in March 2000. The amplicons represent approximately 75% of the genes predicted in the January 2003 release 3.1 Drosophila genome annotation update.
Incyte in-house algorithms were used to develop gene-specific primers averaging 20 nucleotides in length that were used to PCR amplify one exon or exon fragment from every predicted gene in the fly genome. The regions amplified to build the array ranged in size from 150 to 600 bp with an average size of 410 bp. PCR fragments were amplified and each amplicon was quality control tested for DNA concentration, purity, and fragment size. A total of 13,856 unique Drosophila elements are included on the array. Each element was spotted in duplicate(some are spotted multiple times) for a total of 29,222 elements which were distributed on two separate glass slides designated subarrays A and B. In addition to the Drosophila elements, both halves of the array contain non-Drosophila controls elements that serve to orient the arrays, function to correct for background and to provide calibration standards. The total number of elements (Drosophila transcripts and controls) is 31,464. Each array element includes an area of 150 micron diameter with a center to center separation of 170 microns. Adhesion to glass was facilitated by UV crosslinking at 120,000 mj/cm2. Qualification of the arrays was examined by dying representatives of each print run with Syto 61 dye. Dyed slides were read with a GenePix 4000A scanner (Axon Instruments, Foster City, CA) at 535 nm. The April 2007 platform update is based on the Dmel_RELEASE 4.1 re-annotation result from DGRC (https://dgrc.cgb.indiana.edu/microarrays/annotation.html).
Transcription profiling of Drosophila melanogaster SSDP target genes
Data table header descriptions
ID
FLYBASE
Flybase ID assigned by DGRC remapping
FLYBASE_SECONDARY
Secondary Flybase ID assigned by DGRC remapping
RELEASE
D.mel annotation version of DGRC remapping
GENE_NAME
Dmel_RELEASE 4.1 Gene name assigned by DGRC remapping
GENE_SYMBOL
Dmel_RELEASE 4.1 Gene symbol assigned by DGRC remapping
GENE_SYNONYMS
Dmel_RELEASE 4.1 Gene synonyms assigned by DGRC remapping
DGRC.PROBE_ID
Probe ID assigned by DGRC
CHROMOSOME
Dmel_RELEASE 4.1 Chromsome location
TRANSCRIPTS
Dmel_RELEASE 4.1 Transcript assigned by DGRC remapping
START_COORD
Dmel_RELEASE 4.1 Start coordinate of predicted amplicon
STOP_COORD
Dmel_RELEASE 4.1 Stop coordinate of amplicon
LENGTH
Amplicon length
CYTO
Dmel_RELEASE 4.1 Cytological location
GO_MOL_FUNC
GO assignment, Molecular Function
GO_BIO_PROC
GO assignment, Biological Process
GO_CELL_COMP
GO assignment, Cellular Component
R3.1_GENE_NAME
Gene name in Dmel_RELEASE 3.1 mapping
R1_GENE_NAME
Gene name in Dmel_RELEASE 1 mapping
SUBARRAY
Each array includes elements split into two chips designated A or B
LOCATION
Location of element on the subarray
PLATEID
Plate ID for amplicon source used for array elements
PLATEROW
Row location of amplicons on plate
PLATECOLUMN
Column location of amplicons on plate
INCYTECLONEID
Incyte clone ID number used for array
CLONESOURCE
Source of clone
PRIMERS
Sequence of primers used for PCR amplification
STATUS
1 - PCR status, PCR products flagged by Incyte quality control that showed failed amplification, multiple bands, wrong size bands or primer problems, 2 - predicted amplicon not from dmelr3 or mitochondrial genome sequence, but heterochromatin scaffolds, 3 - multiple amplicons predicted, 4 - multiple BLAST hits for amplicon(s), 5 - amplicon(s) map to multiple genome features, 6 - FLAGGED_PROBLEMATIC by Flybase in D.mel annotations
RNA elongation ; GO:0006354, RNA elongation from Pol II promoter ; GO:0006368, chromatin assembly or disassembly ; GO:0006333, intracellular signaling cascade ; GO:0007242, transcription initiation from Pol II promoter ; GO:0006367
CG18647, CG18647, XIV, Biniou, FoxF, Dmbin, l(3)65CEe, Distal W5.4 Group XIV
INC004H01
3L
CG18647-RA,CG18647-RB
6965322
6965735
413
65D6
mesoderm cell fate commitment ; GO:0001710, phosphoenolpyruvate-dependent sugar phosphotransferase system ; GO:0009401, regulation of transcription ; GO:0045449, regulation of transcription from Pol II promoter ; GO:0006357
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