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Platform GPL1404 Query DataSets for GPL1404
Status Public on Nov 01, 2004
Title MJArray Fly
Technology type spotted DNA/cDNA
Distribution non-commercial
Organism Drosophila melanogaster
Description 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.
Contributor(s) Katzenberger JD, Bauer M, Pankratz MJ
Submission date Aug 11, 2004
Last update date Jan 18, 2013
Contact name Michael J. Pankratz
Phone ++49 +7247 82 6087
Fax ++49 +7247 82 3354
Organization name Forschungszentrum Karlsruhe
Department Institute of Genetics
Lab Pankratz
Street address P.O. Box 3640
City Karlsruhe
ZIP/Postal code 76021
Country Germany
Samples (68) GSM28562, GSM28563, GSM28564, GSM28565, GSM28566, GSM28567 
Series (2)
GSE1672 Starvation response in Drosophila and its implication for sex specific metabolism and aging
GSE10625 IPC knockout, 14 day old female flies, 48h yeast feeding

Data table header descriptions
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
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
CYTO Dmel_RELEASE3 polytene chromosome cytological location
SPOT_ID spot identifier

Data table
01_01_01 dActin no dActin
01_01_02 BCE no BCE
01_01_03 spin32kd no spin32kd
01_01_04 spinchA no spinchA
01_01_05 iroquois related homeobox 5 Drosophila no iroquois related homeobox 5 Drosophila
01_01_06 mActin no mActin
01_01_07 IATS 300ng/īl no IATS 300ng/īl
01_01_08 IATS 150ng/īl no IATS 150ng/īl
01_01_09 IATS 100ng/īl no IATS 100ng/īl
01_01_10 IATS 50ng/īl no IATS 50ng/īl
01_01_11 IATS 25ng/īl no IATS 25ng/īl
01_01_12 IATS 10ng/īl no IATS 10ng/īl
01_01_13 IATS 5ng/īl no IATS 5ng/īl
01_01_14 empty no empty
01_01_15 empty no empty
01_01_16 empty no empty
01_01_17 CT34372; ok 386 CG14615 CG14615 [CG14615-RA] CG14615 CT34372 FBgn0031184 33129 NM_134615 X 21382045..21381496 20B1-20B1 yes
01_01_18 CT33647; ok 416 CG17108 CG17108 [CG17108-RA] CG17108 CT33647 FBgn0032285 34471 NM_135595 2L 10685871..10685405 32A2-32A2 yes
01_01_19 CT32919; ok 385 CG13544 CG13544 [CG13544-RA] CG13544 CT32919 FBgn0034826 37673 NM_137917 2R 18183777..18183393 59C5-59D1 yes
01_01_20 CT34381; ok 415 CG14624 EG:BACR42I17.9 [CG14624-RA] CG14624 CT34381 FBgn0040357 31068 NM_166871 X 964384..964886 1E4-1E4 yes

Total number of rows: 32448

Table truncated, full table size 5110 Kbytes.

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp

Supplementary data files not provided

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