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Platform GPL6285 Query DataSets for GPL6285
Status Public on Jan 04, 2008
Title Yale University MCDB Rice japonica NimbleGen 390K Oligo Array version1
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Oryza sativa
Manufacturer NimbleGen microarray system
Manufacture protocol 1. Oligo length: 36
2. Minimum oligonucleotide Tm: 80
3. Maximum oligonucleotide Tm: 95
4. Temperature to use during secondary structure prediction (an oligo will be rejected if it can fold into a stable secondary structure at this temperature): 65
5. Threshold to report putative cross-hybridizations (all targets hybridizing with a given oligo with a Tm exceeding this threshold are reported): 70
6. Minimum oligonucleotide GC content: 40
7. Maximum oligonucleotide GC content: 73 for gene models; 77 for TARs
8. Minimum distance between the 5' end of two adjacent oligos: 1
 
 
Contributor(s) Li X, Wang X, He K, Ma Y, Su N, He H, Stolc V, Tongprasit W, Jin W, Jiang J, Li S, Deng X
Submission date Dec 14, 2007
Last update date Jan 04, 2008
Contact name Hang He
E-mail(s) hehang@gmail.com
Organization name Yale University
Department MCDB
Lab Deng Xing-Wang
Street address 165 Prospect St
City New Haven
State/province CT
ZIP/Postal code 06511
Country USA
 
Samples (8) GSM251113, GSM251116, GSM251118, GSM251120, GSM251124, GSM251127 
Series (1)
GSE9925 Global mapping of epigenetic modifications of histone H3 Lysine 4 di- and trimethylation in Rice

Data table header descriptions
ID
Sel_Crt Oligomer frequency calculated to determine the uniqueness of every 36mer subsequence in the genome
SEQUENCE DNA sequence of the oligonucleotide
CHROMOSOME Chromosome number and strand from which the oligonucleotide sequence was selected
TIGR_START Chromosome start position of the oligonucleotide from version 2 of TIGR rice pseudomolecules
RANGE_GB GenBank ACCESSION.VERSION
RANGE_START the start position (relative to the RANGE_GB accession)
RANGE_END the end position (relative to the RANGE_GB accession)
RANGE_STRAND

Data table
ID Sel_Crt SEQUENCE CHROMOSOME TIGR_START RANGE_GB RANGE_START RANGE_END RANGE_STRAND
41466969 1.000000 CGATAAATAGGCCATCCATTTCACTACGGTTAGATA 4:+ 12917485 NC_008397.1 13269073 13269108 +
41453628 1.000000 TCTAGAGAGTTAGACTATCTCTAATGTTGAGGTGTC 4:+ 10728959 NC_008397.1 11080444 11080479 +
41344936 1.000000 TGGGGGAAAAAGCATAGCATTTGTTTCAAGTTGCTA 10:+ 16193452 NC_008403.1 16180013 16180048 +
41409494 6.000000 CTGAGTTTGCTCACCACCTGTTTCGAGAGGAGAGCA 4:+ 3037700 NC_008397.1 3037650 3037685 +
41606264 1.000000 GAACTTATTCCCAAGAGAGAAGTGCAAAATGCCAAT 4:+ 33455808 NC_008397.1 33993325 33993360 +
41383117 1.050000 GTTCCATGCTTAATTCTAGTGCCTTTAATCTGTGAC 10:+ 21574860 NC_008403.1 21558221 21558256 +
41522428 1.000000 ATATCCTCCAACAGGCAACAGTAGCAAAACATTGAT 4:+ 21345678 NC_008397.1 21826439 21826474 +
41287416 1.050000 TTGACTTTCCTTTCTAAACTAGTGTTCGTTTAGCGC 10:+ 7272362 NC_008403.1 7263823 7263858 +
41489027 1.000000 GCCAAGATATTCCTTGTCAACTTCTACAGATAGAAG 4:+ 16455474 NC_008397.1 16940603 16940638 +
41445738 3.350000 CCGATCATCTCCTGTAACTCCGTCTTGTTCTCTGGA 4:+ 9283213 NC_008397.1 9527020 9527055 +
41463954 9.800000 CTCCTGCAAAAACGGACTCTCTGGAAACATCGGAAT 4:+ 12461780 NC_008397.1 12813468 12813503 +
41291630 1.200000 ACACATCAAGCGATCGTCCTATAACCGTGGACACGG 10:+ 8050778 NC_008403.1 8040439 8040474 +
41505734 1.000000 GTAGTACTCCCCGTCGCTAACCACGCTCGAGGACCT 4:+ 18959973 NC_008397.1 19443632 19443667 +
41342864 1.750000 GCATTCCAAAAAGAGTAAAAACCCAACGCTTCTCAA 10:+ 15878279 NC_008403.1 15864840 15864875 +
41381695 1.000000 AAATTTGGAGTAGAGGGATCTGGAAGTCTCATATTG 10:+ 21383439 NC_008403.1 21367200 21367235 +
41546487 1.000000 ACTGGAAACTTTGCATACTCGCGCTGTCCCCGGCCA 4:+ 24809739 NC_008397.1 25286065 25286100 +
41339146 3.100000 TGGCAGCCGCTCCTCTCCCTTCAACCACCACCGAAA 10:+ 15330824 NC_008403.1 15317385 15317420 +
41243863 2.000000 TATCATCCCAGTTAGCGGTAGTAAAAACATGGATGA 10:+ 389801 NC_008403.1 384662 384697 +
41358420 1.000000 TCTATAAGGTTGCTGCACCTACGGAAGAAGATGACT 10:+ 18091635 NC_008403.1 18077396 18077431 +
41309471 1.000000 AAAAACAAGTGAAAACTAGCGGCAAGTGGAAAGCAA 10:+ 10878791 NC_008403.1 10867552 10867587 +

Total number of rows: 389379

Table truncated, full table size 37447 Kbytes.




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