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Status
Public on Oct 15, 2010
Title
NimbleGen Zmays 120K CGH array [091006_NS_Zmays_CGH_exp]
Technology type
in situ oligonucleotide
Distribution
custom-commercial
Organism
Zea mays Manufacturer
Roche NimbleGen
Manufacture protocol
Roche NimbleGen manufactures custom, high-density DNA arrays based on its proprietary Maskless Array Synthesizer (MAS) technology. The MAS system is a bench top, solid-state, high-density DNA array fabrication instrument comprised of a maskless light projector, a reaction chamber, a personal computer, and a DNA synthesizer. Roche NimbleGen builds its arrays using photo-mediated synthesis chemistry with its MAS system. At the heart of the system is a Digital Micromirror Device (DMD), similar to Texas Instruments' Digital Light Processor (DLP), employing a solid-state array of miniature aluminum mirrors to pattern 786,000 to 4.2 million individual pixels of light. The DMD creates virtual masks that replace the physical chromium masks used in traditional arrays. These virtual masks reflect the desired pattern of UV light with individually addressable aluminum mirrors controlled by the computer. The DMD controls the pattern of UV light projected on the microscope slide in the reaction chamber, which is coupled to the DNA synthesizer. The UV light selectively cleaves a UV-labile protecting group at the precise location where the next nucleotide will be coupled. The patterns are coordinated with the DNA synthesis chemistry in a parallel, combinatorial manner such that 385,000 to 2.1 million unique probe features are synthesized in a single array.
Description
product # OID24389
Contributor(s)
Swanson-Wagner RA , Eichten SR , Kumari S , Tiffin P , Stein JC , Ware D , Springer NM Submission date
Aug 23, 2010
Last update date
Oct 15, 2010
Contact name
Steve R Eichten
E-mail(s)
[email protected] Organization name
University of Minnesota
Department
Plant Biology
Lab
Springer Lab
Street address
1445 Gortner Ave
City
St. Paul
State/province
MN
ZIP/Postal code
55108
Country
USA
Samples (58)
GSM586152 , GSM586153 , GSM586154 , GSM586155 , GSM586156 , GSM586157
GSM586158 ,
GSM586159 ,
GSM586160 ,
GSM586161 ,
GSM586162 ,
GSM586163 ,
GSM586164 ,
GSM586165 ,
GSM586166 ,
GSM586167 ,
GSM586168 ,
GSM586169 ,
GSM586170 ,
GSM586171 ,
GSM586172 ,
GSM586173 ,
GSM586174 ,
GSM586175 ,
GSM586176 ,
GSM586177 ,
GSM586178 ,
GSM586179 ,
GSM586180 ,
GSM586181 ,
GSM586182 ,
GSM586183 ,
GSM586184 ,
GSM586185 ,
GSM586186 ,
GSM586187 ,
GSM586188 ,
GSM586189 ,
GSM586190 ,
GSM586191 ,
GSM586192 ,
GSM586193 ,
GSM586194 ,
GSM586195 ,
GSM586196 ,
GSM586197 ,
GSM586198 ,
GSM586199 ,
GSM586200 ,
GSM586201 ,
GSM586202 ,
GSM586203 ,
GSM586204 ,
GSM586205 ,
GSM586206 ,
GSM586207 ,
GSM586208 ,
GSM586209 Series (1)
GSE23756 Pervasive gene content variation and copy number variation in both maize and its undomesticated progenitor
Data table header descriptions ID Unique numerical identifier
SEQ_ID Sequence ID
CHROMOSOME Chromosome of assayed gene
SEQ_ID Sequence identifier
SEQUENCE Probe sequence
RANGE_START Mb position of assayed gene
LENGTH Length of probe
RANGE_END End position
Data table ID SEQ_ID CHROMOSOME SEQ_ID SEQUENCE RANGE_START LENGTH RANGE_END 1
CHR10RS100098959
chr10
chr10:100098205-100100917
AGATTATCCACTGTGACATAAAGTCCCAGAACATCCTTCTCGATGGCAAC
100098959
50
100099008
2
CHR10RS100099787
chr10
chr10:100098205-100100917
AAGGTCATACCGATGAGCCATGTTGACTGGCCACTGTCTGACTAT
100099787
45
100099831
3
CHR10RS100100245
chr10
chr10:100098205-100100917
CCTCTGGTTACGAATATGATCCGTACTGGTCCATGGATGTGAACA
100100245
45
100100289
4
CHR10RS100100636
chr10
chr10:100098205-100100917
AACAAGATCGGCAACCTTACAGTGACTTGGTATGCCAAGACCAAC
100100636
45
100100680
5
CHR10RS100123453
chr10
chr10:100123370-100125355
TAATTACTTCCTACCTTCGTGGATTGTATGCCTTCCTGCATGTGATATATTTTGTCTCGG
100123453
60
100123512
6
CHR10RS100123569
chr10
chr10:100123370-100125355
ATGGAGGGAGCTCGGACAAGAATATTACAGAATTCGTCGCGAAGTATTCTTTAAGT
100123569
56
100123624
7
CHR10RS100123833
chr10
chr10:100123370-100125355
AACTCGACACTGGAAGCAATTGTTAATGGTGTGCCAATGGTGGCA
100123833
45
100123877
8
CHR10RS100124649
chr10
chr10:100123370-100125355
AGACTGGTGCCCTGTGTTCCTTCGGGCATCACTGCGGCAATTTGA
100124649
45
100124693
9
CHR10FS100303702
chr10
chr10:100303662-100305462
ACCACATCGTGTTCACCACTACCCTCCACTGATTCTGATCACCGG
100303702
45
100303746
10
CHR10FS100304556
chr10
chr10:100303662-100305462
AGGCAGATTATATGGCACTAACATGGCGTGCAAAGACAATAGGCC
100304556
45
100304600
11
CHR10FS100304705
chr10
chr10:100303662-100305462
AAACAGCTTCCGCGTTCTGTTATTCTTGTATCCTACGGTACTGTCTCTAATTACGA
100304705
56
100304760
12
CHR10FS100305371
chr10
chr10:100303662-100305462
AGGTGAGCAATTTGTAGTCAATATTTGTTGGAGGTATCTTCTGAAATGTGGAGCGAG
100305371
57
100305427
13
CHR10FS100339029
chr10
chr10:100338913-100341518
CAGGCACGAAGAGTGGATGGCAAAGTACGACCGCGTCTACAGCGA
100339029
45
100339073
14
CHR10FS100339122
chr10
chr10:100338913-100341518
CCTCATCGAGTCCGTCAACGCCGGCAACCACAAGTTCTGGCTGGA
100339122
45
100339166
15
CHR10FS100339815
chr10
chr10:100338913-100341518
GTATGGCGTCGCCAGCGACGGCACCAAGTATTGGGTCATGAAGAA
100339815
45
100339859
16
CHR10FS100345087
chr10
chr10:100345041-100347565
CCCACCTTCGCGGTGCCCTCGCCTTTGTCCCTCTCACACGCCCGC
100345087
45
100345131
17
CHR10FS100345297
chr10
chr10:100345041-100347565
CAGATCTGGGCCGACTACGACGCCGTCTACGGCCGTCTTCCACCT
100345297
45
100345341
18
CHR10FS100345734
chr10
chr10:100345041-100347565
ATACGCCTGCTGGCGAAGCACCGCTTCGACATCCGCGAGCTGATC
100345734
45
100345778
19
CHR10FS100359708
chr10
chr10:100359696-100360010
CAAGTCGCCATGACGATCGTGCTTGTGCTGCTTGTGGTGGTGGTT
100359708
45
100359752
20
CHR10FS100359767
chr10
chr10:100359696-100360010
GTCTGCTCCGGAGCTGGCGTCGACCGGCAGCACCGAGGTGGCTGG
100359767
45
100359811
119609 14332 Kbytes .Supplementary file Size Download File type/resource GPL10846_091006_NS_Zmays_CGH_exp.ndf.gz
9.0 Mb
(ftp) (http) NDF
GPL10846_091006_NS_Zmays_CGH_exp.ngd.gz
437.2 Kb
(ftp) (http) NGD
GPL10846_091006_NS_Zmays_CGH_exp.pos.gz
1.4 Mb
(ftp) (http) POS
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