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Platform GPL8945 Query DataSets for GPL8945
Status Public on Jun 30, 2010
Title ISU_Minion_Mhyo_IG-oligo_v1.0
Technology type spotted oligonucleotide
Distribution non-commercial
Organism Mesomycoplasma hyopneumoniae
Manufacturer Chris Minion Laboratory at Iowa State University
Manufacture protocol Probes were designed for the intergenic regions of Mycoplasma hyopneumoniae. Intergenic regions were defined as noncoding DNA sequences between annotated genes in the M. hyopneumoniae genome sequence (GenBank accession # AE017332). Intergenic regions larger than 50 bp were considered for analysis, and those between 125-450 bp were considered for PCR-based probes. Oligonucleotides were designed for some intergenic regions based on the inability to produce PCR products or the length of the region (50-125 bp). Oligonucleotides ranged in size from 50 to 60-mers and were synthesized by Integrated DNA Technologies, Inc. (IDT, Coralville, IA). Oligonucleotides were resuspended to 100 pmol/μl in nuclease free water and then 9 μl were vacuum dried and diluted to 30 μM in IDT Epoxide spotting buffer. These oligonucleotides were spotted to Corning Epoxide substrates in triplicate.
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Coating other
 
 
Contributor(s) Minion FC, Gardner SW
Submission date Jul 28, 2009
Last update date Jun 30, 2010
Contact name Chris Minion
E-mail(s) fcminion@iastate.edu
Phone 515-294-6347
Fax 515-294-8500
Organization name Iowa State University
Department VMPM
Street address 1130 Vet Med
City Ames
State/province IA
ZIP/Postal code 50011
Country USA
 
Samples (4) GSM446980, GSM446982, GSM446983, GSM446985
Series (1)
GSE17893 Mhyo IG Rnd vs MhRnd

Data table header descriptions
ID
size size of oligonucleotide
SEQUENCE oligonucleotide sequence
ORF locus tags
Start start position on M.hyopneumoniae genome sequence, AE017332
Stop stop position on M.hyopneumoniae genome sequence, AE017332
GENOME_ACC GenBank accession to which locus tags correspond
GC % GC content of sequence
Tm melting temperature in C
Notes comments about probes
SPOT_ID spot identifier

Data table
ID size SEQUENCE ORF Start Stop GENOME_ACC GC Tm Notes SPOT_ID
ig-001.F1 60 ATTAAACAGCTTTTTGGGCAAAAAGTACTATAAATTAAAGTGGTTTTTTATCTTTTCTAC 1397 1456 AE017332 25 62.62851525 This column has notes on the probes INTERGENIC_REGION: ig-001.F1
ig-001.F2 60 TATTATTTTTATTATTAAAACTAAATAAAAATTAACTAAATATAATATAATTATTAAAGG 1470 1529 AE017332 6.666666667 55.16024113 INTERGENIC_REGION: ig-001.F2
ig-002.F1 52 TAAATTTTCTCTAAAATTTAGACTATTTTTTGATTAAAATTCAAAAAAATAA 2671 2722 AE017332 11.53846154 56.67664046 INTERGENIC_REGION: ig-002.F1
ig-002.F2 52 GCTATTTTATAGTATAATTTAAAAAAAAGAAACTAATTTGAGGAAATTTTTA 2723 2774 AE017332 15.38461538 57.10675078 INTERGENIC_REGION: ig-002.F2
ig-006.F1 53 TAAATAATAAAAAAGGAAAAGTAGGCGAAAATTACTAATTTTTTCCTTTTTTT 7051 7103 AE017332 18.86792453 59.7933953 INTERGENIC_REGION: ig-006.F1
ig-006.F2 52 TAATAAAAGGCTAAAAAAAATTAATATTGGTGGATGTTGAAAGGAGAAACTG 7104 7155 AE017332 26.92307692 61.54015602 INTERGENIC_REGION: ig-006.F2
ig-007.F 60 TTTATTAAGAACTGAACGGAAAAAAGTAATTTTAATTTATAATTTAATAAAATTATAAAA 7739 7798 AE017332 11.66666667 58.27866006 INTERGENIC_REGION: ig-007.F
ig-008.F1 60 ATTTTTTACCTAATTTTTAACAAATAAGTAAAAATTTAAGTATTTTTTCTAATTTTTTCA 8827 8886 AE017332 11.66666667 58.83962259 INTERGENIC_REGION: ig-008.F1
ig-008.F2 60 AATAAATTTGGTTAAATAAATTTTCCATTTTTGTAAAATTTATTTAACAAAAATGGAAAA 8912 8971 AE017332 13.33333333 60.06811537 INTERGENIC_REGION: ig-008.F2
ig-013.F 60 TTTTTTTTTTTTTTTTTAAAGGTTTCGACTGCAAAAAAAAAAAAAAAAAAGTATCCAAAG 14689 14748 AE017332 18.33333333 62.18224653 INTERGENIC_REGION: ig-013.F
ig-016.F2 60 TCAAAAAAAAAAAAAAAAAGTATAATATAAATAAATATAAAAAAACGGAGGCATTAAAAC 17663 17722 AE017332 15 59.70367536 INTERGENIC_REGION: ig-016.F2
ig-016.R1 60 AATTTATTAAAATTTAATTATTACAAAAAAAATATTTTCCATAATTAAAATAGATAAAGA 17652 17593 AE017332 8.333333333 57.2098175 INTERGENIC_REGION: ig-016.R1
ig-020.R1 60 AATTATTTCAAATAAGATGACATTTCTAGTTGAAAAGTTGGTTGGTAAAAATCAGTTTTA 19967 19908 AE017332 23.33333333 62.43338975 INTERGENIC_REGION: ig-020.R1
ig-020.R2 60 AAAAATATCTAAAATATAAATTAATAATTTAACCAAAAAAACAGTTATAAAATTATTCTT 20044 19985 AE017332 10 57.73249151 INTERGENIC_REGION: ig-020.R2
ig-021.R1 60 AATTATTTAAATTACTATTAAAAAAATTAAAACAACTAATTAAAATTTCGAATAATTGTA 22407 22348 AE017332 10 57.90797009 INTERGENIC_REGION: ig-021.R1
ig-021.R2 60 GAATGAAATATATACAAAACGTTAAGGTTTTTTTGAAAAGGGACCCAAAAACACAAAAAA 22504 22445 AE017332 26.66666667 63.79800545 INTERGENIC_REGION: ig-021.R2
ig-022.R 60 TCAAAATTTTATTAAAAAATATGATTATGAATTACTAAAAGTAAAAAATATGAATAATTT 24832 24773 AE017332 10 57.81464295 INTERGENIC_REGION: ig-022.R
ig-025.R1 57 AATAAAGATTTAATGAAATGCAAAAAAACGGATAACAAGGAGGAATTTTTCTAAAAG 30482 30426 AE017332 24.56140351 62.17769392 INTERGENIC_REGION: ig-025.R1
ig-025.R2 56 TAAAAATTTTTAAATTTTTATGAAAAAATGATTATAAATACTAAAAATAATAGGAT 30538 30483 AE017332 8.928571429 56.48349371 INTERGENIC_REGION: ig-025.R2
ig-031.F1 60 AAAATTATCCTTTAATTTATGTTATTTTTTAAAAATTTGTCATATCTTTTGGGAATAATT 38353 38412 AE017332 15 59.85116228 INTERGENIC_REGION: ig-031.F1

Total number of rows: 528

Table truncated, full table size 75 Kbytes.




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