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Platform GPL8944 Query DataSets for GPL8944
Status Public on Jun 30, 2010
Title ISU_Minion_Mhyo_IG_v1.0
Technology type spotted DNA/cDNA
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. PCR primers were designed using the Primer3 online software program. PCRs were performed in 96-well plate format in a MJ Research Dyad thermocycler (Bio-Rad Laboratories, Inc. Waltham, MA) in 100 μl reactions using the following conditions: 1X MgCl2-free PCR buffer (Invitrogen); 3.5 mM MgCl2; 0.2 mM each dATP, dTTP, dGTP, and dCTP (NEB); 200 pmol of each primer (IDT); 2 units Taq polymerase (Invitrogen); and 100 ng M. hyopneumoniae strain 232 chromosomal DNA obtained via phenol-chloroform extraction. Thermocycler conditions started with a denaturation at 95ºC for 5 minutes followed by 30 cycles of denaturation at 94ºC for 1 minute, annealing at 56ºC for 1 minute, and elongation at 68ºC for 30 seconds and ending with a final elongation at 68ºC for 10 minutes. Products were confirmed by 1.2% agarose gel electrophoresis and purified via Mobio’s UltraClean PCR Clean-Up Kit according to manufactures protocol. Purified PCR products were quantified by visual inspection, dried via vacuum centrifugation, and resuspended to approximately 200 ng per μl in Corning spotting buffer (Corning). Products suspended in spotting buffer were electrophoresis in 1.2% agarose gels to confirm purity and concentration of each product. The PCR product microarrays were spotted to Corning UltraGAPS glass substrates in triplicate by the University of Iowa DNA facility.
Support glass
Coating aminosilane
 
Description Corning UltraGAPS substrates (catalog #40016)
 
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 (2) GSM446977, GSM446978
Series (1)
GSE17893 Mhyo IG Rnd vs MhRnd

Data table header descriptions
ID
lprimer left primer sequence
rprimer right primer sequence
start start position on M.hyopneumoniae genome sequence, AE017332
stop stop position on M.hyopneumoniae genome sequence, AE017332
size size of PCR product
GENOME_ACC GenBank accession to which locus tags correspond
ORF locus tags
SEQUENCE PCR product sequence
lcomment Notes about left primer and product
rcomment Notes about right primer and product
SPOT_ID spot identifier

Data table
ID lprimer rprimer start stop size GENOME_ACC ORF SEQUENCE lcomment rcomment SPOT_ID
ig-016.1 TTGCCTCTTTATCTATTTTAATTATGG TGTTTTAATGCCTCCGTTTTT 17588 17723 136 AE017332 TTGCCTCTTTATCTATTTTAATTATGGAAAATATTTTTTTTGTAATAATTAAATTTTAATAAATTCTTTTATTTTTCAAAAAAAAAAAAAAAAAGTATAATATAAATAAATATAAAAAAACGGAGGCATTAAAACA INTERGENIC_REGION: ig-016.1
ig-019.1 GGAACCAAAAACTTAAATTTCCAAT GCTTTTTCGGGAAATTCAGA 19402 19639 238 AE017332 GGAACCAAAAACTTAAATTTCCAATATGTTTGAATTTAAGTTTTTTACAAGTCACTAGTAAACCTATATAAAATATTATTAGGGCTAAAATTGGAATATAGTTGATCAAATAATTGAAAAACTAGTGTGATTTTCTATGTGTATGTTAATTTTGTAGAATCCTGATGTGAAATCCTTTTGTAAATTTCAGGAAAATAATTGGAACTATAAAAATAAAATCTGAATTTCCCGAAAAAGC 142205 ctttttcgggaaatt 142219 INTERGENIC_REGION: ig-019.1
ig-024.1 CGGTTTTATAAGTTAGGTTTGTTGG AACAAAAGTGGTGTAATCAAAATCA 27990 28144 155 AE017332 CGGTTTTATAAGTTAGGTTTGTTGGGTTTTAACTTAAATTTTATTATGCAATAATTTTACCAAAAAAAAAAAAAAAAAAAAGAAGTAAATAAATTAGTAGAAAAAATTCAGACAATTAGTTTTTTATCTATGATTTTGATTACACCACTTTTGTT 369382 aacaaaagtggtgtaatcaaaatca 369358 INTERGENIC_REGION: ig-024.1
ig-027.1 TCCCTTTTTGTTTGAATTTGG TGTTGAATTTGAGGCAAACA 33661 33955 295 AE017332 TCCCTTTTTGTTTGAATTTGGTCTAGATTTTGCTTATTATCTTAATTATTTGATTATTTGTACAATTTCACTTCTATTAGAAATTAAAATAAGAATGGATACTATAATTTTAACAAAAAAAAAAAAAAAAAAAAAACCAAGAAAAAGAAAAAATAAGGAAAGAAGAATATTTATAAAACATTGAATGATATTGAATTATTTGCAAATATCAGAATAAAAGGTCACTTTTTTACTAAATCAAATTATTTTATTATAGAATTTTATATTAATTAGTATGTTTGCCTCAAATTCAACA 723995 tttttgtttgaattt 724009 INTERGENIC_REGION: ig-027.1
ig-028.1 ACTTTTTGGGGGAGAAGTGG TCAAGTGGTTGAATGCTTTTTG 34601 34768 168 AE017332 ACTTTTTGGGGGAGAAGTGGACAAGCAAAAAATATTAAAACTTGCAAAATCTCTCTATTTTGTCCCAAATGAGAAGGTAATTTATACAATTTTAACTGAAAAAGATCAAATGTTAGCTCGAATTAACTATTTGCACCAGTTTGATACAAAAAGCATTCAACCACTTGA INTERGENIC_REGION: ig-028.1
ig-030.1 GGTAAAACTCAGGATTTTCCAA TTCTACCTTATTTTTACGCTTTTT 37663 37843 181 AE017332 GGTAAAACTCAGGATTTTCCAAAAAAATTAATTTATTTTTTTGGAAAATTAAGTAAACCTTTTTCATTAAAATTTTAGTAATTCGTAAAAATGAGTTAAATATTAAAATTTTAAATGTTTTTTAATTTTAGTAGTCGACAAAATTTTTGATTTTTTAAAAAAGCGTAAAAATAAGGTAGAA INTERGENIC_REGION: ig-030.1
ig-035.1 TCCTTTCTGAAAATGCGTAAA TGCGAATCTCCATTTCTTTT 46173 46369 197 AE017332 TCCTTTCTGAAAATGCGTAAAAATTTTTCTAAATTAAATTTTATACAAAAAGGTAAATAATTTTACAAAAATTTTAATGTAAAATTTAAAAAAAGTGGTAAAATTACTAAAAATAATTAAATTTTGTTAATTTTTTGTTTTTTTAGTACCAAAACTCAAAATAGACAAAATTAATATAAAAGAAATGGAGATTCGCA INTERGENIC_REGION: ig-035.1
ig-057.1 TTTGTAAATTTAAAGCAGAATTACAGG AAGCACACCCAACTGAATCC 67413 67558 146 AE017332 TTTGTAAATTTAAAGCAGAATTACAGGTAGTAATTGTATCAGAAAAAGATTAAATTGTTTTTAATTTTTAATTTTATGATATAATTTAATTCTTAAACTCAGAATAAATAAAAATATCATTAAAATGGATTCAGTTGGGTGTGCTT INTERGENIC_REGION: ig-057.1
ig-072.1 TTTTCCGGTTTTGGAATTTG TTTGGCCTCAGCTTGTTTTT 90926 91175 250 AE017332 TTTTCCGGTTTTGGAATTTGATCAAACAGGAAAATTTAATAAAGCGGGTTGAAAAAATAAAAAAAAACTTTAAAAAAAGAAAAATAAGGTATAATTTATGGCAAAACAAGATTTTTATAAAATTCTGGGAGTTGAAAAATCAGCATCACTAACAGAAATAAAAAAAGCTTATCGAAATTTAGTAAATATTTATCATCCTGATAAAAATACAAAAAAATCAGCTGAAGAACAAAAACAAGCTGAGGCCAAA INTERGENIC_REGION: ig-072.1
ig-072.13 CCGCTTTTGATCAGCAATTT TAGCGCCTGAACCCTTACAG 91252 91503 252 AE017332 CCGCTTTTGATCAGCAATTTGGTGGTGGGTCTAGTGGCTTTTCAGGATTTGATTTTGGCGACATTTTTTCAAGTTTTACCTCTGGTTTTGGTTTTGGTGGCTCACAAGAACAAAAATATAGTCGTCCTTTAAAGGGCGAAAATTTTCAAGCTAAAATTTATATCAGTTTTATCGAGTCAATTCTTGGAAAAGAAATCTCCCAGAAATTAACAAAATACGATCAATGTGATAACTGTAAGGGTTCAGGCGCTA INTERGENIC_REGION: ig-072.13
ig-088.1 GGCGTTCAATTGTTTCGTTT CCGACACCGTTGTTTTCATA 104386 104687 302 AE017332 GGCGTTCAATTGTTTCGTTTTGTGACATTTTACCTTTTAATTTAACAATTTTAGTTAATTTTTTAGTTCTTAATATAAATAGTAAAAAAATTTACTATTTTTTACTTAAAATTTTTCCACTTTTTATTCAATTATAACATATTCTAATTTTTCTTTGTTAAATATACAGTGAATTAATTAACTAGGATAAAATTTAGCTGTTATTTTTTAAAAAAAAGGTAACCTAAAAAAATTTGTGACTGAGACCTTTTCTTAAAGGGTCTTTTTTTTGTTTTTAACAAATATGAAAACAACGGTGTCGG 654198 ccgacaccgttgttttcata 654179 INTERGENIC_REGION: ig-088.1
ig-088.r1 TTGTTCTTTGTTTTCAATGAATTTT CCCTTTAAGAAAAGGTCTCAGTCA 104357 104645 289 AE017332 TTGTTCTTTGTTTTCAATGAATTTTTTGAGGCGTTCAATTGTTTCGTTTTGTGACATTTTACCTTTTAATTTAACAATTTTAGTTAATTTTTTAGTTCTTAATATAAATAGTAAAAAAATTTACTATTTTTTACTTAAAATTTTTCCACTTTTTATTCAATTATAACATATTCTAATTTTTCTTTGTTAAATATACAGTGAATTAATTAACTAGGATAAAATTTAGCTGTTATTTTTTAAAAAAAAGGTAACCTAAAAAAATTTGTGACTGAGACCTTTTCTTAAAGGG 654156 ccctttaagaaaaggtctcagtca 654133 INTERGENIC_REGION: ig-088.r1
ig-093.1 GCTATGGAAAAATTAAAATTCCAAAAA CCATATTTCAAACTTAAAACAAAAA 109140 109346 207 AE017332 GCTATGGAAAAATTAAAATTCCAAAAAAACTTTTATTTTGGAATTTTTTTGATATAATAATTTTGCTTTTTTAAATTAAATCTTTTTTTTGGGAAACGACTTGCTGAATTTTATTTTTTATGTTTTGCCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACTTGAAAAATTTTTGTTTTAAGTTTGAAATATGG 21975 ttcaaaattaaaacaaaaa 21957 INTERGENIC_REGION: ig-093.1
ig-100.1 AAAAAGTTCTACCAATTTTTGATTTC AAGAAATCCTTTGCGACATT 115727 115995 269 AE017332 AAAAAGTTCTACCAATTTTTGATTTCTAATTTAATATAATTATATCATAAAATCACAAAAAATTTATTGATTTTTAGCCTTATTTATTAGGACTATTGAGGGGGGTTTTTGACTATTAATCAAAAAAATACTATAAAAACGTAGTTTTTTTGATTAATAGAAAAATTTATTTTCACTAAAAGTTTCAAAAATAATAAATTGGAAACCTTTTAATAAATTAACTAAATTTTCTTGAAATTAAGTTATAATAATGTCGCAAAGGATTTCTT INTERGENIC_REGION: ig-100.1
ig-106.1 TTTTTACTCGGGTTTAAATTAATCAG AGTTCACCTCCGCGAATTTA 123426 123643 218 AE017332 TTTTTACTCGGGTTTAAATTAATCAGATTTAATAACATGAAATCACCTAAATTATCCTATAGAAAAAAATTCTAAACTATAAGTATTCTTAGATCTTGAATAATTTAGTGGCTTCTAATAATTTTTGGTTAAAATCACAATCCTTTTCGGATTTTAGTTACTAAAAAATTAAAATATGGTACAATTTTAATTAAATTGTAAATTCGCGGAGGTGAACT INTERGENIC_REGION: ig-106.1
ig-106.11 TCTCGATTCTAAATATTGGTTTTCTT TCAACCTTGAATTTCTATAAGCA 123154 123399 246 AE017332 TCTCGATTCTAAATATTGGTTTTCTTAAGAATTAAAATTTTATTATTTCAATTACTTAATTATAATGTTTATCAATTATACTATAATAGGTAAAAATTTTCAAAAAATATACTTTAAAATTCCTACATTTTTTTAAAAAAATGTTTAAAAATAGCAACTTTTTACCTTTTAGCTAATAAAAATAAACAATTTTTTATAACTTTTAATGTCTTCAAGTTAGACTTGCTTATAGAAATTCAAGGTTGA INTERGENIC_REGION: ig-106.11
ig-109.1 TGGATTGGGTCTTTGAAGTTG TTCATTAATCCGCAAAGGTCT 130316 130457 142 AE017332 TGGATTGGGTCTTTGAAGTTGAAGTTCAGGAGTATCTATCCCAAAAAGTCGAAAATGACGGTTGTTTTTATCAGTAAAAGTATCACCATCATAGACATCTTTTACAAAGGTTGTATATTTTAGACCTTTGCGGATTAATGAA INTERGENIC_REGION: ig-109.1
ig-134.1 TTAAAAATCAAGACTTGGTAACTAAAA AAAATTTAAAGAATATTACCAACAAGG 160885 161009 125 AE017332 TTAAAAATCAAGACTTGGTAACTAAAAATACTATAAAATAAAGTACTTTTTGCATTTTCAGTTGTCAGCATCATCTATTAGTAAATTAAAAAACATTACCTTGTTGGTAATATTCTTTAAATTTT INTERGENIC_REGION: ig-134.1
ig-139.1 GCTTTTCCTTTCTCGAGTTTACA TCATCTTTAGTCACGCTTTTATGG 167658 168047 390 AE017332 GCTTTTCCTTTCTCGAGTTTACAATTATATCATATTTTAATAATATGAATAAGTATTTTTATGGTTTTTTTGACGAAAAGGTTAGAAGAAAGCTAATTAACAAAAATATTATCAAATTTTTCAAAATTTTCAAGCTTTTCTTATAAATTTTTTAATATAAATTAGTTAGAATTTTAATTAGTGAAAAAAATTATGAAATCCGAAAAACTTATTAAAAAATTCCTTCCATATTTCTTTAAAGTTTGACCATTTTTTGGATGTTTTTAAAAAATAATTGGGTATATTTTAATATTTTTTTAATGATTTAATAATTTAATATGTTTTTTATATTATTGTGCAAAAATATATTTAAATATAATAAAATTACCATAAAAGCGTGACTAAAGATGA INTERGENIC_REGION: ig-139.1
ig-141.1 TGATTCAGAGTGGGAAGAAAAA AAGCTGTCCCCGCTAAAACT 169681 169832 152 AE017332 TGATTCAGAGTGGGAAGAAAAATTTTTAAAATTACAAAATGAAACAAAGGAATCAAAGAAGCAATTTGAGAAATTTTTAGGTAAATATCAAAGATTTTATAATGCAACAAAAGGGCTAAATATAACATCTGCAGTTTTAGCGGGGACAGCTT INTERGENIC_REGION: ig-141.1

Total number of rows: 236

Table truncated, full table size 76 Kbytes.




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