title: NimbleGen Human 385 K array V1.0
status: Public on Jul 06 2010
contact.city: Omaha
contact.first: Himabindu 
contact.last: Ramachandrareddy
contact.email: hramacha@unmc.edu
contact.state: NE
contact.address: 600 South 42nd st
contact.department: Pathology and microbiology
contact.country: USA
contact.institute: University of Nebraska Medical Center
contact.phone: 402-559-7921
organism: Homo sapiens
description: The coordinates of the genomic regions tiled on the custom chip are based on assembly hg18.
  Genomic regions of genes having a critical role in B cell differentiaion were tiled
manufacture_protocol: NimbleGen manufactured a custom array by maskless array synthesis technology with 387,981 45- to 55-mer oligonucleotides tiling portions of >100 genes, chosen on the basis of their likely role in B-cell differentiation. We included as little as 10 kb surrounding the promoter for some genes; several hundred kb for others; and, for a few, only evolutionarily conserved portions of large regions. The region to be included was based in part on the genome-wide data available from T-cells, on the distance to neighboring genes, and the extent of evolutionary conservation in distant regions. Probes average 50 nt in size and overlap adjacent probes by 25 nt. Reverse strands were also tiled on the chip but displaced by 12-13 nt. A custom algorithm was used to eliminate oligonucleotides from repetitive elements likely to crosshybridize.