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Platform GPL3448 Query DataSets for GPL3448
Status Public on Feb 16, 2006
Title YALE/NIMBLEGEN_HUMAN-CHR22_372K_v1.0
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Homo sapiens
Manufacturer NimbleGen Systems, Inc.
Manufacture protocol Maskless array synthesis [1] was used to construct isothermal arrays. This array contains oligonucleotides that start every 85 bp and tiles the entire nonrepetitive part of human chromosome 22 (human genome build NCBI35/hg17 was utilized). Repetitive elements were identified using RepeatMasker [2] and oligonucleotide probes were designed to represent the nonrepetitive DNA sequence. The oligonucleotides were designed to be of variable length, adjusted to match a target melting temperature of 76°C according to the following formula: Tm = 81.5 + 16.6*(log10([Na+])) + 0.41*(%GC) - 600/length. Probe lengths were constrained to be a minimum of 45 bp and maximum of 85 bp.

[1] Nuwaysir, E.F., Huang, W., Albert, T. J., Singh, J., Nuwaysir, K., Pitas, A., Richmond, T., Gorski, T., Berg, J. P., Ballin, J. et al., Genome Res., 2002. 12: p. 1749-1755, PMID: 12421762, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=search&term=12421762

[2] Smit, A.F.A., Hubley, R. & Green, P., RepeatMasker Open-3.0, 1996-2004.
 
 
Contributor(s) Urban AE, Korbel JO, Selzer R, Weissman SM, Hacker A, Emanuel BS, Cubells JF, Richmond T, Green R, Popescu GV, Gerstein MB, Snyder M
Submission date Feb 13, 2006
Last update date Feb 16, 2006
Contact name Jan Oliver Korbel
Phone +1 203 432 5405
Fax +1 203 432 5175
URL http://bioinfo.mbb.yale.edu/array/
Organization name Yale University
Street address 266 Whitney Avenue
City New Haven
State/province CT
ZIP/Postal code 06520
Country USA
 
Samples (24) GSM96607, GSM96608, GSM96609, GSM96610, GSM96611, GSM96612 
Series (4)
GSE4240 High Resolution Mapping of DNA Copy Alterations in Human Chromosome 22 Using High Density Tiling Oligonucleotide Arrays
GSE6010 High-resolution comparative genome hybridization survey of healthy individuals (chromosome 22)
GSE12731 Evaluation of the amplicons for detection of known CNVs using Cs22 HR-CGH

Data table header descriptions
ID
CHROMOSOME Chromosome
STRAND Strand
GB_RANGE Genbank-accession.version[start_coordinate_on_sequence..end_coordinate_on_sequence]
BUILD Human genome build
X x position of feature on microarray
Y y position of feature on microarray
SEQUENCE Sequence of isothermal oligonucleotide

Data table
ID CHROMOSOME STRAND GB_RANGE BUILD X Y SEQUENCE
CHR2200P000212218 CHR22 FORWARD NC_000022.8[35435738..35435801] NCBI35/hg17 1 1 TCAGCCTTGCTTTTTTTCTTTTGCTTGTCTCTTTCCTCTTTATGTATATATCCCTCTCCCATCT
CHR2200P000353724 CHR22 FORWARD NC_000022.8[48082270..48082314] NCBI35/hg17 25 1 CCATGGTGTTAGTCATGGAGGGCCTGAGCCCAGTCTGAAAAGTAC
CHR2299P000348655 CHR22 REVERSE NC_000022.8[47726586..47726630] NCBI35/hg17 27 1 CCTGGGAGGGAGAAGCCAATTCGGTATCTCAACTTAGGCATGTCT
CHR2299P000160321 CHR22 REVERSE NC_000022.8[29876675..29876719] NCBI35/hg17 29 1 CCCACCAGGACCGGGGGCTCCACCCCCACCTGTTGGCAGAGCAGC
CHR2200P000029550 CHR22 FORWARD NC_000022.8[17808966..17809028] NCBI35/hg17 31 1 TATAAATCGAATTATGCCTCCCAGCACACTTTAGACTAAACTCTAAACTCCGTATCAAAAGGC
CHR2299P000210811 CHR22 REVERSE NC_000022.8[35310287..35310331] NCBI35/hg17 33 1 GGCTTCCTTTTAACACCCCAAGATGCAGGAGGGCAGAGGGGCCAT
CHR2200P000109232 CHR22 FORWARD NC_000022.8[24809605..24809658] NCBI35/hg17 37 1 GTTGTATCATCCTCTCAGACTTTCCGTGAGAATCAAACAGGGCATTATGAACAT
CHR2200P000063572 CHR22 FORWARD NC_000022.8[20626196..20626240] NCBI35/hg17 39 1 TCCAGGCCCCACACCTGGGCCTCCCTGCCAGCACCCACTCAGCAT
CHR2299P000222267 CHR22 REVERSE NC_000022.8[36230844..36230888] NCBI35/hg17 41 1 AGTGTGCACTGCTTCGAAGGGCCAGGGGCCCGCCCCCTGGGGCAG
CHR2299P000303335 CHR22 REVERSE NC_000022.8[44044473..44044517] NCBI35/hg17 43 1 CGCCGGCCAAAGGCCTCCCGCACCCCCAGCCCATACCTTGGTCTT
CHR2299P000345469 CHR22 REVERSE NC_000022.8[47457139..47457183] NCBI35/hg17 45 1 GCTCCATCCCTGCCCCCCTGGTAAGCCCACTTTTGCTCACTAAGC
CHR2200P000002024 CHR22 FORWARD NC_000022.8[14635858..14635902] NCBI35/hg17 47 1 CCTGCTCGGCCATGGTGGTGAACCTATAGCCACGCTCGGTGAGGA
CHR2299P000156025 CHR22 REVERSE NC_000022.8[29477825..29477869] NCBI35/hg17 49 1 CTCCACTGGAATCATTTGGGATTCATATGGCAGGGGGGACGCAGG
CHR2299P000080043 CHR22 REVERSE NC_000022.8[22023853..22023906] NCBI35/hg17 51 1 GCTCTTGGCCTATGAAGACTTTACGGTGCTGTGTTCGCAAAATATAAAAGGTAA
CHR2200P000366938 CHR22 FORWARD NC_000022.8[49104128..49104172] NCBI35/hg17 53 1 GGCACATGTGCCTCACACCGTTCCTTGCCCTCATCTGGTTGTCTT
CHR2299P000139245 CHR22 REVERSE NC_000022.8[27871023..27871074] NCBI35/hg17 55 1 AATGCTACTAAGACGGAAATAAATGGGATCTGCAGCTTCACTGTTGCGAAAG
CHR2299P000328363 CHR22 REVERSE NC_000022.8[46018771..46018815] NCBI35/hg17 165 1 CTTTGCATGCACTCTCACAATTGCCCACCAAAAGGAAGTCACAGA
CHR2299P000236081 CHR22 REVERSE NC_000022.8[37508165..37508210] NCBI35/hg17 167 1 TGGTTTGCACATAGTGGGAACTTGGGAGATAGTGGTTTGTTTGGCT
CHR2200P000044494 CHR22 FORWARD NC_000022.8[18876404..18876448] NCBI35/hg17 169 1 TCTAGACTGCACCTTGAGGGCCAAAAACGTCCAGATTTCCTGCTC
CHR2200P000145660 CHR22 FORWARD NC_000022.8[28462582..28462627] NCBI35/hg17 171 1 AACTTCCTCAGATCATCAACCCTGTTACTCTCTGAAGTTCTGCCTG

Total number of rows: 372352

Table truncated, full table size 48665 Kbytes.




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