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Platform GPL13655 Query DataSets for GPL13655
Status Public on Oct 01, 2011
Title NCSU_Thermotoga species
Technology type spotted DNA/cDNA
Distribution non-commercial
Organisms Thermotoga maritima; Thermotoga neapolitana; Thermotoga petrophila; Thermotoga sp. RQ2
Manufacturer NCSU Kelly Group
Manufacture protocol Probes were initially designed based on open reading frames from the published genome sequence for T. maritima. Additional probes were designed based on T. sp. RQ2/T. maritima suppressive subtractive hybridization results (Nesbo et al, 2002), a TIGR draft sequence of T. neapolitana, and the published genome sequence for T. petrophila. All probes were generated by PCR amplification of genomic DNA, purified using QIAquick kits (Qiagen), and resuspended in 50% dimethyl sulfoxide to 100 ng/ul. DNA was printed onto UltraGAPS slides (Corning) with five replicates for each probe using a Genetix QArray Mini.
Support glass
Coating aminosilane
 
Description Because some probes were designed based on SSH results, some probes duplicate the same ORF or cover intergenic DNA. Here is a key for the notation used for probe names: TRQ2_0171a means there is more than one probe for this ORF, TRQ2_1842-1843 means this probe covers part of 1842 as well as part of 1843 and any intergenic DNA in between, TRQ2_1803-1820739-1820933 means that this probe covers the genome coordinates listed. The probe may cover part of the indicated ORF or it may only cover intergenic DNA in the vicinity of that ORF.
 
Submission date May 26, 2011
Last update date Oct 01, 2011
Contact name Andrew Frock
E-mail(s) adfrock@ncsu.edu
Phone 9194950054
Organization name North Carolina State University
Department Chemical and Biomolecular Engineering
Lab Hyperthermophile
Street address 840 Main Campus Drive, Partners II, Room 3304
City Raleigh
State/province NC
ZIP/Postal code 27606
Country USA
 
Samples (8) GSM731853, GSM738020, GSM738021, GSM738022, GSM1144374, GSM1144375 
Series (2)
GSE29557 Thermotoga species transcription on glucose and a mix of polysaccharides
GSE47072 Thermotoga maritima transcription during exponential and stationary phase growth on 1 and 5 g/l yeast extract

Data table header descriptions
ID
ORF
Genome coordinate start
Genome coordinate end
SEQUENCE
SPOT_ID

Data table
ID ORF Genome coordinate start Genome coordinate end SEQUENCE SPOT_ID
CTN_0026 CTN_0026 21128 21355 AGACAACGGTTCGAAAGATTCCACTTTGAAAATCTTGGAAGAATATCGTAGCAGAGAACCAAATTTTATATACATTCCCCTTGGAAAAAACACAGGTACAACTTTCTCGAGGAACATAGGGATACGCATAGCACGTGGAAAGTATATTGGAATTCTTGATTCAGATACGATGGTTCCAAAAGGAACTATAAAAAAGATAATTGACGCTTTCCAGGAAATACCATCAAA
CTN_0027 CTN_0027 21796 21883 GAAAATCGTGAAGAAGATAGCAAGGAGGAAATTTGATTTCGTTTGTTTTAAAAATTCTCCTGAAAATGCTCCTCGTGGTCATGGAAAA
CTN_0028 CTN_0028 22816 23074 GAAGTTGGGAAAAAACGAGTCCAGATGATAAGAGACAAAGCTTTTGTGTTTAACAACAGATTGTTGTTTCTTGGAACCTTAAATTATTATCCGAATGAAATAGCTGCTATCAGACTGGTCGAAAAAATCTTTCCACAAATACTGAAACACAAAAAAGATCTGGAATTGTACATAGTGGGGTCGAATCCTTCAAATAAACTAAAAAGGCTATGTGGGAATAATGCAAAAATAAAATTGCTTGGTTACGTTGAGGATTTGC
CTN_0029 CTN_0029 23536 23816 AGAATAGGCACAGATTGGGAACCATACTATGAATTTTTTCATCTTCCCTCATATAAATTGATGTTGGAACATTATTTTGAACCCCTTTATAAACTGTTGGCAATTATTGTGAAATTGTTATTCAACAATTATTATGCATTTTTATTCGTTATAGGTTCTTTTTTCCTGGTAGAAACTTACACCGTAAACAAAATAGCACTTGAGACAATGAAACCAAGGGGATATAGCTCTACAATTTTATTGCTGGCTATTTACATGTTCAGGTTTGCAGATTACATGGG
CTN_0030 CTN_0030 24598 24825 TGGTGCCAAAAACAGTTGCCATTTTAGTGAGCTATAACGGTTTCCATGACACAGTAGAATGCGTAAAAACTCTGCTTAATCAAACGGTACCACTACATAAGATAGTGATTGTTGATAATGCTTCTCCTAACAATGACTATGAAAAACTCAAAGAAGTATTCTCAAACGAATCCAAGGTGGTTGTTCTCAAGACCCCAAAGAACGGTGGTTTCGCCTATGGTAACAACT
CTN_0031 CTN_0031 25529 25787 CATTGCGCGCAAAGGCATCATCCTCGCTGGTGGAGCTGGAACACGCCTGTACCCTATGACCCTTATAACTAGTAAGCAACTGTTACCCATATATGACAAGCCCATGATCTATTATCCGCTCACCACGCTCATGCTGGCTGGAATAAGAGAGATTCTTATCATATCAACACCCAGGGATCTTCCAAATTTCCAGAGACTTCTCGGTGATGGAAGTCAATTTGGAATTTATCTCGAATACGCTGAGCAATCTGAACCAAGG
CTN_0032 CTN_0032 26427 26639 TGAAGGTCATGGAAACAGATTTGCCAGGAGTTTTGATTATAGAACCCAGAGTCTTTGAAGACGAACGTGGCTGGTTCATGGAAAGTTATTCTTACAGAGTATTCAAAGAGCTTGGAATAGATGCTGTGTTCGTCCAGGATAATCACTCCTACTCTAAGAGAAAAGGAACTCTCCGGGGAATACACTTCCAGAATAATCCGGTGGCACAGGCAA
CTN_0033 CTN_0033 26990 27193 TGAAAATTCTCGTCACAGGTGGAGCAGGATTCATAGGAAGCAACTTTATACACTACATGATGGAAAAACATCCAGATTACAGAATTATCTGTCTTGACAAGCTCACCTACGCTGGAAATCTAAGAAACCTGGAAAGTGCGTTGAATAGAGAGAATTTCCGCTTCATAAAGGGAGACATATGTGACAGGGAACTGGTCTACAAGG
CTN_0033-0034 CTN_0033 27816 28192 ACCCGGACACGATAGAAGATATGCCCTCGACATCACGAAGATGAAGGAAGAATTCGGCTGGTCACCAAAGATTTCTTTTGAGGAAGGACTCAGAAGCACTATAAAGTGGTACCTTGAAAACAGAAACTGGTGGGAAGAAATTATAAACGGTGAATATATGAAATACTACGAAAAGATGTATGGGGAGAGATTGAAAGAATAAATAAGAGCTAGTGGGATTGAGGGGGTGATTAGGTGATTTCCATAGTTTGTGTCTATAACAAAAAAAACATTTTAAATGAGTATCTAATAAAAAGTTTAGAAATCCAAACCTACAGTGATTATGAGCTTATACTGCTGGATAACCGAAGAAATAAATACAAATCCGCCGCTACTGC
CTN_0034 CTN_0034 28267 28522 CGACGGTTTTGTCGGATATTGTTGAGATATTATCATCAAATTCAAGAAAACAGGAAGCAATTTTTGGAGTAGCTGGTCGTGATCCAAAAAAAGGTGTTTTGACAAACATCACCCACGGTTATCCACCAGTAAGAGCTGGTGAGGAGAATGTGAAAAATGATGTTATAGAAGTACAAACCGTTGATGAATGTCTTTTTATTATTCCGAGATCATTATTTGAAAAATTAAGATTTGATGAAACAACAATTGACGGCTG
CTN_0036 CTN_0036 29997 30380 TCATTTGCTCTGACAATTGTGCCTTCCAATTTACGAACATTCTTTAACTTTCTCTATCAAGCAATGGGAGAATTTTCAGTATACTCAAAAATTGCAGTCATTTATCCAATCAGCTTGCTTACATTTAATTTGATTATAATATTTGTCCTTAATTCGAAAAGTTATATTCCTTTTGTAATATCTTATCTAATAGCACTTTATCTTCCATACCTTGTATATGAAATAGAATACAATCGCTCGTTTAAAATAAACAATGTCGCTGTTGGAAAAGATTTTTCTGAAATAAAGATGTTGTTTAAAATAGGAATATTTATAATGCTCGGAAATCTTTCAACACTTCTCGTTTACTCTTTAGACAGGTGGTTCGTCAAGTTGTGGCTTACA
CTN_0039 CTN_0039 33013 33244 TTTCGTTAGGTACCTGGTTTCGTGCGATAATTGGTTTCATTTCCACTCCCGTCATCAGCTACTTGATCGTGCCCGAAGAGTTCGGCCGTGCTTCGATGTTCACGTTAGTGTACAATGTAGCTCTGCTGTTTTCCCTTCTTGGACTTGATCAGAGTTTTGTAAGGTATTACTACGAAAAACAGGACAAGAGTGAAACCTTTTGGAACTGTCTAATACCCTCCGTTGTTTTCGG
CTN_0039-34638-34712 CTN_0039 34638 34712 CCTTCCACAGTTCCATCAGATAGCAGAGTCTTTCTTCAATTTTTGTTGTATTATCATTCACTCCCATTCTGATGT
CTN_0044 CTN_0044 38459 38593 TGTGGGGATACAAGCTTTGTCCAGTTCAAGGGCATGGTCCATGAGTTCTTCAGGGATTTCAAAGTGTCTGGAAAGTTCTTCGAGCAGATCTGCTATGGAACGTTCCCATGCCTGTGCTCCCATTTTCTGGAACAC
CTN_0045 CTN_0045 38795 38880 CTTATAACCTGGGATTTGCACACCGAACTCTCCCTGGATGGTGTGAAAATAAAAGTTCTGCCTGCCTATCTCTTTTTGCTCGACGC
CTN_0045-38989-39067a CTN_0045 38989 39067 ACTGTTGTTTTAATGCTCTTCGGGGTGGCTCTTCTGGGAAACGAAGTGTGGTTTTTCTTCGATCCTGTATTTTCTGTCC
CTN_0045-38989-39067b CTN_0045 38989 39067 ACTGTTGTTTTAATGCTCTTCGGGGTGGCTCTTCTGGGAAACGAAGTGTGGTTTTTCTTCGATCCTGTATTTTCTGTCC
CTN_0046 CTN_0046 39132 39343 GGACACTGTTCTCATCCGCGGAATTGGATACACAGCGTCTATGTCTGATCCTTCGAACATCGAAATCTTGGCTTTTGGAGGGGAGATTTCGTACAATCGATATTTCAAAGAAGTTTTCAACGGAGGATATGTTGGTGTGTCACTTGGTTATTCTTTGATAACATACAAACTCAACGACACATCTCTTAACATTCACGCGCCTGTTTTTGGTG
CTN_0046-39621-39692a CTN_0046 39621 39692 GGACGGTGAAGATCCAGAGCGTTTCTCATGCCAGCAGGGTACGCTAAAGACCCAACCACCAGATCTCTTCCC
CTN_0046-39621-39692b CTN_0046 39621 39692 GGACGGTGAAGATCCAGAGCGTTTCTCATGCCAGCAGGGTACGCTAAAGACCCAACCACCAGATCTCTTCCC

Total number of rows: 2583

Table truncated, full table size 1055 Kbytes.




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