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Platform GPL6335 Query DataSets for GPL6335
Status Public on Jan 15, 2008
Title Yale University MCDB Medicago truncatula NimbleGen 390K Oligo Array
Technology type in situ oligonucleotide
Distribution non-commercial
Organism Medicago truncatula
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 Dec 31, 2007
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) GSM254078, GSM254079, GSM254080, GSM254082, GSM254083, GSM254084
Series (2)
GSE10055 Transcriptional Analysis of 1M Regions in Medicago truncatula 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 medicago 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
35635453 1.000000:Tiling ACATTGCTAACAATTTATGCCAACCCTAATCTTGAT MD:- 479358 479393 -
35467358 1.000000:Tiling ATTATGAGTAGTTTAAATAATTAGAATAATTAAACT MD:+ 593947 593982 +
35646655 1.000000:Tiling TTGGTTTTTGGTGTGGACCTGATGCGTCGGTTGGAT MD:- 537680 537715 -
35719341 1.000000:Tiling AGTTTATATTATGGACCACATACATTATTAATTGAA MD:- 973430 973465 -
35670369 2.000000:Tiling AAAGTTGTTTGCATAAAAGCTTCTTCATTCAATTCA MD:- 686856 686891 -
35427339 1.000000:Tiling TTGAGGAACTTTTTGCTTTCATATATTTGTGTTGAT MD:+ 385283 385318 +
35582532 1.000000:Tiling TGTTGCTGTTTGTTATTTAACTAAGCTGCATGAGTC MD:- 202556 202591 -
35368562 1.000000:Tiling TGATTGATATCTTGCAGATACAACGTGAGTTAAACA MD:+ 73471 73506 +
35381129 1.000000:Tiling TCAATGATTTGGGCGGGATATTCTGGTGATTTAGAT MD:+ 141385 141420 +
35579734 1.000000:Tiling GGTCTAGTTTGAGTGTAGTATCGCGTGACGACTAAA MD:- 186847 186882 -
35521543 1.000000:Tiling TATAAGCCACTCATGAAAGTGTTTTTTAGCAACCTA MD:+ 927086 927121 +
35377295 1.000000:Tiling TTTGGGTTAATTATTAATGTTTCTTAGCCAATGACA MD:+ 120420 120455 +
35705538 1.000000:Tiling TCGACGCCGCCACCTGGGGCGTCAACGTTCAACCTT MD:- 895108 895143 -
35720929 1.000000:Tiling GAGGTCCTCTGTGTGCAGAATTTCCTTACATAGCAG MD:- 981498 981533 -
35441308 1.000000:Tiling TAGTTTCTTTATGTTTAACGGGGTCTTACAATAAAG MD:+ 458853 458888 +
35361535 1.000000:Tiling TGGCCATGTTCATCATCATGTATACTCAGCACACAG MD:+ 36993 37028 +
35709642 1.000000:Tiling ATGTTGATGGAATATTAACAAAATGTCAAAATTAAA MD:- 916309 916344 -
35598311 1.000000:Tiling TGACTTGGATTCTTCAAATCACATTTAATTCCTTGT MD:- 284743 284778 -
35471953 2.000000:Tiling TTAAGTCAAATAACTTGCGTAGAAAATAATCCCTCC MD:+ 623027 623062 +
35706030 1.000000:Tiling ACCTAGTCATTAGTAAGTAAACGTGGGAACAAGAAG MD:- 897715 897750 -

Total number of rows: 380570

Table truncated, full table size 30804 Kbytes.




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

Supplementary file Size Download File type/resource
GPL6335-Bacs-Description.pdf.gz 9.0 Kb (ftp)(http) PDF
GPL6335.txt.gz 314.2 Kb (ftp)(http) TXT

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