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Platform GPL6337 Query DataSets for GPL6337
Status Public on Jan 15, 2008
Title Yale University MCDB Glycine max NimbleGen 390K Oligo Array
Technology type in situ oligonucleotide
Distribution non-commercial
Organism Glycine max
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
BAC fasta and description files linked as supplementary files
 
 
Contributor(s) Li L, He H, Zhang J, Wang X, Stolc V, Tongpraist W, Yu O, Deng X
Citation(s) 17439305
Submission date Jan 02, 2008
Last update date Apr 16, 2008
Contact name Hang He
E-mail(s) [email protected]
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 (6) GSM254085, GSM254086, GSM254087, GSM254088, GSM254089, GSM254090
Series (2)
GSE10056 Transcriptional Analysis of 1M Regions in Glycine max Using Tiling Microarrays
GSE10151 Transcriptional Analysis of Medicago truncatula and Glycine max Using Tiling Microarrays

Data table header descriptions
ID
Sel_Crt Oligomer frequency calculated to determine the uniqueness of every 36mer subsequence in the assemblied soybean BACs
SEQUENCE DNA sequence of the oligonucleotide
Strand strand
START the start position of BAC sequence file
END the end position of BAC sequence file
RANGE_STRAND

Data table
ID Sel_Crt SEQUENCE Strand START END RANGE_STRAND
35419538 1.000000:Tiling AGACAATGTATGAGGAGCTTGTTTAACCAGAGTGTG AX:+ 336485 336520 +
35557696 1.000000:Tiling TTTCCCTTTCCTTTAATTTATTGGAAGTTTACATTT AX:- 102574 102609 -
35566271 1.000000:Tiling TTACATTAGGGATGTATTGAAAATCACAATGGAAAT AX:- 146954 146989 -
35641987 1.000000:Tiling ACGTATCATAATAATATTTAATTAGTAACCATAATA AX:- 538368 538403 -
35603913 1.000000:Tiling TCTACAGCTTCACCACGTAACTCACACAAGGTAATA AX:- 342012 342047 -
35509624 1.000000:Tiling GTAATAACCAAATGCATAATTCAATTTACCTTGGGT AX:+ 832252 832287 +
35572013 1.000000:Tiling CTCATTTGTCCACTCCTCTTTGACAACTGAGGCAAC AX:- 176642 176677 -
35471763 1.000000:Tiling TGCAAATGCAGAAAATGAAGTCTTCAGTTCGTTCAA AX:+ 605827 605862 +
35412535 1.000000:Tiling ATTGATTCAATCGTTGATTATAATAATTGTAATTTG AX:+ 299784 299819 +
35628970 1.000000:Tiling TTGTTTTGCTTTCATTTTTTATAATTGTAAATAATT AX:- 471253 471288 -
35676194 1.000000:Tiling TTTAGATATTTTTTTACCTTAAAAAATTGTTTTTAT AX:- 727612 727647 -
35674402 1.050000:Tiling TTTAGAGAATAAAAATACATTAAAACTAAAAAAATA AX:- 717824 717859 -
35657192 1.000000:Tiling ACGTGTAAACATCCAATGGATACCTCATTTTCTCCA AX:- 617021 617056 -
35452102 1.000000:Tiling TATCTTTCCCTTGTCCAAGCATATACGAGGAGCCTG AX:+ 504542 504577 +
35477664 1.000000:Tiling TAGCACTAATTAGACCACATGGTTTCAGTTATGTTT AX:+ 636175 636210 +
35454293 1.000000:Tiling TAACAATAACTTTTTACATATTTATTTATCTAATTT AX:+ 515869 515904 +
35611499 1.000000:Tiling TGCAACAATTAAGATCAAAGACTTGCCCCACAAAAA AX:- 381081 381116 -
35675048 1.000000:Tiling AAGTTGTAGGTGCATCAACGGTCCATGTTGGTTAGC AX:- 721527 721562 -
35541988 1.000000:Tiling TGATCCTTCCATTCCTCATGCTTTATGGGAGTCTGC AX:- 21677 21712 -
35404752 1.000000:Tiling CTTAGTGAAAATGATTATTTTACATTCAACGAATAT AX:+ 259628 259663 +

Total number of rows: 366798

Table truncated, full table size 29646 Kbytes.




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

Supplementary file Size Download File type/resource
GPL6337-Bacs-Description.pdf.gz 7.7 Kb (ftp)(http) PDF
GPL6337.txt.gz 292.4 Kb (ftp)(http) TXT

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