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Platform GPL7344 Query DataSets for GPL7344
Status Public on Jul 10, 2009
Title Rice NimbleGen 390K tiling array (2006-11-14_ggb_rap1_3tile_101706)
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Oryza sativa
Manufacturer Greengene Biotech
Manufacture protocol The profiling was conducted with the Rice 3'Tiling Microarray designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp). Among these, 20,507 genes were from representative RAP1 sequences with cDNA/EST supports and 6,941 genes were predicted without cDNA/EST supports. Ten 60-nt long probes were designed from each gene starting 60 bp ahead the end of stop codon and with shifting 10 bp so 10 probes cover 150 bp in the 3' region of the gene. Genes from chloroplast (123) and mitochondria (74) and selection markers such as gfp, gus, hyg, bar, and kan are included. In total, 270,000 probes were designed with the average size of probe is 60-nt long to have its Tm value 75 to 85 ¡ÆC. The microarray was manufctured at NimbleGen inc (http://www.nimblegen.com/). Random GC probes (38,000) to monitor the hybridization efficiency and four corner fiducial controls (225) were included to assist with overlaying the grid on the image.
Support glass
 
Description Rice genome build information requested but not provided.
 
Web link http://www.ggbio.com
Contributor(s) Kim Y
Submission date Sep 19, 2008
Last update date Jul 10, 2009
Contact name Nam-gun Kim
E-mail(s) side2000@gmail.com
Organization name GGBIO
Street address Myongi Univ.
City Yong in
ZIP/Postal code 449-728
Country South Korea
 
Samples (67) GSM362291, GSM362292, GSM362293, GSM362294, GSM362295, GSM362296 
Series (7)
GSE14508 Gene expression in S1 panicles of Ubi1:AtJMT transgenic plants and drought-treated nontransgenic rice plants
GSE31855 Expression analysis of RCc3:OsNAC9 and GOS2:OsNAC9 transgenic rice plants
GSE31856 Expression analysis of RCc3:OsNAC5 and GOS2:OsNAC5 transgenic rice plants

Data table header descriptions
ID PROBE_ID column of .ndf file
PROBE_DESIGN_ID
CONTAINER
DESIGN_NOTE
SEQ_ID
ORF
PROBE_SEQUENCE
MISMATCH
MATCH_INDEX
FEATURE_ID
PROBE_CLASS
POSITION
SPOT_ID

Data table
ID PROBE_DESIGN_ID CONTAINER DESIGN_NOTE SEQ_ID ORF PROBE_SEQUENCE MISMATCH MATCH_INDEX FEATURE_ID PROBE_CLASS POSITION SPOT_ID
RANDOM00111681 4850_0382_0780 RANDOM RANDOM_GC15_GC43 TTAGTCCTGCGCGTCCTAAAGCGGTGTTATCTATACTGTTGCATAATCTTCGCACGCTCT 0 65446220 65446220 0 RANDOM_GC15_GC43
3tileprobe_144013 4850_0384_0780 BLOCK1 AK064046 AK064046 gcttcccgaccacacgccatggcatcgggttcccactctcgccgcgctaatatttagtag 0 65089342 65089342 27769633
3tileprobe_138877 4850_0386_0780 BLOCK1 AK121867 AK121867 gagtgcgtgagtacatcaggtctgcccagagttgctgagagagggcaaatcggtggatga 0 65084206 65084206 21269684
3tileprobe_240317 4850_0388_0780 BLOCK1 Os10g0395400 Os10g0395400 gccgccatggccgtcatgccggagacggaggaggtggtcgcgttcacgaggttcctccaa 0 65185646 65185646 12748683
3tileprobe_249788 4850_0390_0780 BLOCK1 AK063113 AK063113 gctacgaaaattccccgcatttccctcaaatgtcaaccacattttccccctttttttcaa 0 65195117 65195117 18927331
3tileprobe_137141 4850_0392_0780 BLOCK1 AK060744 AK060744 aatgtcaaccgtgacattgacattataaatttggtgtgtagtaatgcaataattatgtgc 0 65082470 65082470 18597295
3tileprobe_172797 4850_0394_0780 BLOCK1 Os06g0696900 Os06g0696900 tgcacaaggacgacatcaccctctggtccgtcgacggcgccaccgtcgccatcgtacgtc 0 65118126 65118126 28765495
RANDOM00053875 4850_0396_0780 RANDOM RANDOM_GC15_GC43 TATTGGAGGTACAATCCAAGACAGAGTAACCTTTAAGGCCGGTTTCCAAGCTAATGGTCG 0 65388414 65388414 0 RANDOM_GC15_GC43
3tileprobe_267027 4850_0398_0780 BLOCK1 AB027123 AB027123 tgaaagtcttttgcctttgttttttgcaagttatttctgaaactctctggagagcatgac 0 65212356 65212356 23003261
RANDOM00015523 4850_0400_0780 RANDOM RANDOM_GC15_GC43 GACGTCGCCATCAGTTAGTACACGTGCGACCCTAGTTGCCTGCCCGATAATTAATGGGTA 0 65350062 65350062 0 RANDOM_GC15_GC43
3tileprobe_155556 4850_0402_0780 BLOCK1 AK106373 AK106373 tcacatcgcccgatcgccgtgaccgagtcctgcactggcgacacgagtggtcgagtgcta 0 65100885 65100885 5155052
RANDOM00112440 4850_0404_0780 RANDOM RANDOM_GC15_GC43 TCAGACGATAGGGCGCATGAAGGCTCCTCACCCGACTTGACCTGTTCTGGTCCACCCTGA 0 65446979 65446979 0 RANDOM_GC15_GC43
3tileprobe_54726 4850_0406_0780 BLOCK1 AY345232 AY345232 gccggccattgcaccggttgggttggtcgcagcagtcaacctatcgacaccatgggcgtc 0 65000055 65000055 26544050
RANDOM00108148 4850_0408_0780 RANDOM RANDOM_GC15_GC43 GTATCATTTGGTACTCGTGGTAGGAGACTGATATTACTCCCAGATGTGCGCGGAGCTTTT 0 65442687 65442687 0 RANDOM_GC15_GC43
3tileprobe_213598 4850_0410_0780 BLOCK1 AK100234 AK100234 agctcccccggcgcccggccatcgtcactgcatattaatttctgctggctgctgatatat 0 65158927 65158927 2030503
3tileprobe_265341 4850_0412_0780 BLOCK1 AK068902 AK068902 ttgggaagagaattctgtcaaaaacttacctgaagaacaggaagcactaatcttgcacct 0 65210670 65210670 18356250
3tileprobe_230628 4850_0414_0780 BLOCK1 AK073900 AK073900 atcgttctgcacaactacaccagattcattatggtccgcacgggcagcaagcctgagatc 0 65175957 65175957 9151661
3tileprobe_176006 4850_0416_0780 BLOCK1 AK121080 AK121080 ttcgtgaaagggctcgcaagatagctcgaaagaggcaacaacaacaataaatacatggac 0 65121335 65121335 4351272
3tileprobe_32247 4850_0418_0780 BLOCK1 Os01g0265000 Os01g0265000 cggatggcgcccgccgagccgtggggggacctccgcctgctgtggcgcacggcggcggcc 0 64977576 64977576 9018435
RANDOM00114398 4850_0420_0780 RANDOM RANDOM_GC15_GC43 ATAAGCAAAGTAGGAACTAATTTATGCCAGGTATTCGACCGGGTAGTAATTCCAATCAAC 0 65448937 65448937 0 RANDOM_GC15_GC43

Total number of rows: 390811

Table truncated, full table size 58623 Kbytes.




Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp

Supplementary file Size Download File type/resource
GPL7344.ndf.gz 19.0 Mb (ftp)(http) NDF

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