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| Array design description | |||||||||
| FORMAT | |||||||||
| ARRAYBATCH | Simon Rasmussen, Henrik Bjørn Nielsen and Hanne Jarmer*. (2009) The transcriptionally active regions in the genome of Bacillus subtilis, Molecular Microbiology, 73, 1043–1057 | The array design specification consists of the description of the common features of the array as the whole, and the description of each array design elements (e.g., each spot). Following terminology used in MAGE, we distinguish between three levels of array design elements: feature - the location on the array, reporter - the nucleotide sequence present in a particular location on the array, and composite sequence - a set of reporters used collectively to measure an expression of a particular gene, exon, or splice-variant. The details that should be given of each of them are described below. | |||||||
| ARRAYBATCHNAME | Tiling Array | * array design name | |||||||
| ARRAYTYPE | Nimblegen | * platform type: in situ synthesized, spotted or other | |||||||
| SPOTPARAMID | BaSysBio Bacillus subtilis T1385K array version 1’ | database ID | |||||||
| NUMBERBLOCKSPERCHIP | * physical dimensions of array support (e.g. of slide) | ||||||||
| NUMBERBLOCKSHORIZ | 385000 | * number of features on the array | |||||||
| NUMBERBLOCKSVERTIC | |||||||||
| NUMBERROWSINBLOCK | |||||||||
| NUMBERCOLUMNSINBLOCK | date of production | ||||||||
| SPOTTINGDATE | |||||||||
| COMMENTS | something like surface and coating specification etc | ||||||||
| PROVIDERID | Nimblegen | * availability (e.g., for commercial arrays) or production protocol for custom made arrays | |||||||
| ARRAY | single array of certain array batch | ||||||||
| ARRAYID | SOM03GN9 - SN: 1=M9_Glu_OD=0.4_Repl_2 | ||||||||
| SOM03GNE - SN: 2=M9_Glu_OD=1.0_Repl_2 | |||||||||
| SOM03GNC - SN: 3=M9_Glu_OD=1.4_Repl_2 | |||||||||
| SOM03GND - SN: 4=M9_Glu_OD=0.4_Repl_1 | |||||||||
| SOM03GNF - SN: 5=M9_Glu_OD=1.0_Repl_1 | |||||||||
| SOM03GNG - SN: 6=M9_Glu_OD=1.5_Repl_1 | |||||||||
| SOM03GNH - SN: 7=M9_Glu_OD=0.4_Repl_3 | |||||||||
| SOM03GNJ - SN: 8=M9_Glu_OD=1.0_Repl_3 | |||||||||
| SOM03GNK - SN: 9=M9_Glu_OD=1.5_Repl_3 | |||||||||
| ARRAYBATCHID | |||||||||
| SUPPORTID | |||||||||
| COMMENTARE | |||||||||
| SLIDE_NB | |||||||||
| REPORTER | oligo/sequence on array , related information, common for all arrays in one batch | ||||||||
| RPROBEID | database ID | ||||||||
| SPOTPARAMID | database ID, foreign key to arraybatch | ||||||||
| TYPE | synthetic oligo-nucleotides | * the type of the reporter: synthetic oligo-nucleotides, PCR products, plasmids, colonies, other | |||||||
| STRAND | single stranded | * single or double stranded | |||||||
| SEQUENCE | |||||||||
| LENGHT | Simon Rasmussen, Henrik Bjørn Nielsen and Hanne Jarmer*. (2009) The transcriptionally active regions in the genome of Bacillus subtilis, Molecular Microbiology, 73, 1043–1057 | * approximate lengths if exact sequence not known | |||||||
| PROBETYPE | oligo, cDNA etc | ||||||||
| ACC NUMBER | * gene name and links to appropriate databases (e.g., SWISS-PROT, or organism specific databases), if known and relevant | ||||||||
| PROVIDER | |||||||||
| PROVIDERID | o sequence accession number in DDBJ/EMBL/GenBank, if exists | ||||||||
| ORGANISM | NCBI Accession number | ||||||||
| CHROMOSOMENR | |||||||||
| CHROM_BAND | |||||||||
| SYMBOL | standartized name of gene | ||||||||
| PLASMIDNR | |||||||||
| SYMBOL | |||||||||
| AMPLIFICATIONPROTOCOLID | database ID, foreign key to amplification protokol (separate) | ||||||||
| PURIFICATIONPROTOCOLID | database ID, foreign key to purification protokol (separate) | ||||||||
| PRODUCTIONDATE | |||||||||
| DNAYIELD | amount of DNA on the spot | ||||||||
