The array was assembled using amplicons that were obtained using the Incyte primer set. The set is identical to the one used to produce platform GPL20, primer sequences can be viewed in that platform. We included a reference to the ID of GPL20. The amplicons represent 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.
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 11,796 reactions led to a single product of correct size and sufficient amount (marked as ok in column GENE_NAME). The 675 reactions that produced multiple products were run on a gel again and the band of the correct size was excised cloned into pCR TOPO 2.1 (Invitrogen). The 2034 reactions where no band was visible was also subjected to a 'blind' clone-attempt. Those 2709 cloning-reactions led to 2033 positive clones, that were included on the array and marked as 'clone!' in column GENE_NAME. Non sequence-verified clones were not included in the current study. A mixture of all these 2033 clones was used to make a titration dilution as a hybridisation control (Incyte Amplification Titration Standard, IATS) that is included in each of the 48 blocks of our array. Arrays were spotted with a Omnigrid 100 (GeneMachines) with 24 SMP3 pins (Telechem). By having two identical subarrays next to each other on each slide, we obtain 48 blocks with 26 rows and 26 columns each. Spot to spot spacing is 150 micron, average spot diameter is 100 micron.
IPC knockout, 14 day old female flies, 48h yeast feeding
Data table header descriptions
ID
Dmel_RELEASE1_Gene_name
Dmel_RELEASE1 gene name or prediction identifier, CTxxxx, followed by a comment on PCR amplification success, ok: product of correct size and sufficient amount, m: multiple products obtained, no: no product, clone: product was cloned into pCR TOPO 2.1 (Invitrogen)
ID_GPL20
corresponding ID of GPL20, initial platform that made use of Incyte's primer set.
GENE_NAME
Dmel_RELEASE3-1 gene name or prediction identifier, CGxxx - translated gene, TExxx - transposable element, CRxxx - various RNAs, pseudogenes, miscellaneous curator's observation
GENE_SYMBOL
gene symbol or prediction identifier according to Flybase Dmel_RELEASE3-1
TRANSCRIPTS
Dmel_RELEASE3-1 mRNA or prediction identifier(s)
R1_GENE_NAME
Dmel_RELEASE1 gene name or prediction identifier
R1_TRANSCRIPT
Dmel_RELEASE1 mRNA or prediction identifier
GENE_SYNONYMS
Dmel_RELEASE3-1 synonymous gene models, i.e. may indicate splits or merges
CLONE_ID
Flybase identifier
GENE
Entrez GENE ID
GB_ACC
RefSeq identifier, multiple may exist for a given gene, check LocusLink for additional identifiers
GO_IDS_AND_TERMS
Gene Ontology(GO) identifiers paired with their text "terms"
ALTERNATE_GENE
Dmel_RELEASE3-1 alternate gene or prediction identifier to which predicted amplicon maps equally well and has same given genome location as the representative gene
GENOME_LOCATION
Dmel_RELEASE3 chromosome or GenBank accession for contig from which amplicons derived
RANGE
Dmel_RELEASE3 nucleotide range for predicted amplicons