title: AntrHuman20kv03
status: Public on Dec 23 2006
contact.city: Nijmegen
contact.first: Gys
contact.middle: de
contact.last: Jongh
contact.email: G.deJongh@Derma.umcn.nl
contact.state: Gelderland
contact.address: Rene Descartesdreef 1
contact.department: Dermatology
contact.country: Netherlands
contact.web_link: http://www.ncmls.nl/
contact.institute: Nijmegen Centre for Molecular Life Sciences
contact.phone: +31243614093
organism: Homo sapiens
description: Oligonucleotide sequences are available via www.ensembl.org after agreeing to Compugen's conditions
manufacture_protocol: A 19 K oligonucleotide set consisting of 18,861 oligonucleotides representing 18,664 unique sequences (synthezised and sold by Sigma-Genosys,Cambridge,UK . Designed by Compugen,San Jose, CA,USA ,http://www.cgen.com/ , http://www.labonweb.com/ , Catl# HUMLIB384 )was printed (spotting solution:3 x SSC, pH7.0 , 1.5 M betaine ,12 fmol/spot)onto UltraGAPS glass slides (Corning , Schiphol-rijk ,The Netherlands),using an Omnigrid 100 arrayer (Genomic Solutions,Michigan,Ann Harbor USA) equipped with 32 SMP3 pins (ArrayIt , California , Sunnyvale , USA).The program CloneTracker (Biodiscovery , http://www.biodiscovery.com/index/clonetracker )was used to control the printing robot.Printed slides were dried overnight and cross-linked with UV light at 600 mJ using a Strata-linker 2400 Stratagene (Virginia, Glenville, USA).
  For quality control of the chip itself the grid for finding the spots was defined outside the printing area of the robot.Description is “Nothing printed,undisturbed background”.For quality control of the printing robot and the printing process the pins were cleaned and dried in the usual way,dipped in an empty well of the 384-well high throughput plate and a spot was printed.Description is “empty”.
  Cy5 and Cy3 labelled random nona-mers were printed to assist in the visual alignment of the grid for finding the spots on the raw *.tiff image. (Amersham , http://www.amersham.com/ , custom made).
  The SpotReport Alien Oligo Array Validation System( http://www.stratagene.com/manuals/252270.pdf , Stratagene Europe , Gebouw California , Hogehilweg 15 , 1101 CB Amsterdam Zuidoost,The Netherlands )was printed to allow normalisation and calibration of the microarray.This system consists of : Human β-actin oligo , GB_ACC = X63432 , Poly(dA)40–60 oligo , Human COT-1 , Spotreport oligo 1 till 10.
  The Raw image files were collected with a GenPix 4100A laser scanner.
  For a visual interpretation of the *.Tiff files with the raw data the array should be viewed from above,the side where the oligo’s were printed,with a small side of the rectangular array at the top.This is the picture that was produced by the GenePix software.The GenePix software uses the variables “Block” , “Row” and “Column” to indentify the spots.The Genepix software sorts the output data on 1) “Block” , 2) “Row” and 3) “Column” , ascending.We added the variable “KeySpot” .The variable "KeySpot" is an unique address for the spots on the array. It was computed from the GenePix variables "Block" , "Row" and "Column" as : KeySpot = Column + Row x 100 + Block x 10,000 The variable "KeySpot" can be used as a Primary Key to link data base tables.The variable "KeySpot" was also used as the mandatory variable "ID" for the GEO data base at the NCBI.
  
  The array consists of 48 subgrids.
  Subgrids are organised in 12 rows of 4 columns.
  The subgrids are numbered in the normal "reading direction" in the variable "Block" from upperleft =1 to lower right = 48
  The features in the subgrids are organised in 21 rows , numbered in the variable "Row" , of 20 columns , numbered in the variable "Column".
  The rows are numbered from top=1 to bottom= 21.The columns are numbered from left=1 to right=20.
  This pattern was printed in two printing sessions. In the first printing session the print head , equipped with the first 4 x 8 =32 pins , was used to print all the features in Block 1 - 32. In the second printing session the print head , now with the first 4 x 4 =16 pins , was used to print all the features in Block 33 - 48.
  The print head of  the arrayer should be viewed from behind , the position in which it printed the oligo’s on the array.It was equipped with the the first 32 (16) pins arranged as 8 x 4 (4 x 4) pins numbered the normal "reading direction" in the variable PinNum from upperleft =1 to lower right =  32 (16 ).
  The number of the pin that printed a particular spot can be determined from the Block Number with the VB Excel formula  : MOD((Block-1),32)+1 or an equivalent modular function in an other language.
  The variable ID , together with this description , makes all other spot reference variables on the array redundant.We did not include them in the GEO data base. If you would still like to have them , please feel free to email us directly.