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Platform GPL5907 Query DataSets for GPL5907
Status Public on Dec 13, 2007
Title JCVI PFGRC Yersinia pestis 25K v3 array designed primarily based on strain CO92
Technology type spotted oligonucleotide
Distribution non-commercial
Organism Yersinia pestis
Manufacturer JCVI PFGRC
Manufacture protocol 3QYP, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000
Support glass
Coating aminosilane
 
Description This set includes 4826 oligonucleotides, has 25392 spots distributed in 48 blocks.
 
Web link http://pfgrc.jcvi.org/descriptionPages.shtml
Submission date Sep 18, 2007
Last update date Dec 13, 2007
Contact name PFGRC JCVI
E-mail(s) jli@jcvi.org
Phone 3017957840
Organization name J. Craig Venter Institute
Department PFGRC
Street address 9704 Medical Center Drive
City Rockville
State/province MD
ZIP/Postal code 20850
Country USA
 

Data table header descriptions
ID
SEQUENCE Oligo sequence
GC% GC content of the sequence
Internal Repeat Score Internal repeat score
Self-Annealing Score Self-anneal score
Primary Strain The strain of primary target
Primary Target Locus primarily hit by the oligo
Common Name of Primary Target Common name of primary target
Gene Symbol Gene symbol
Strain CO92 Target map of strain CO92
Strain KIM Target map of strain KIM
ORF primary target linkin Entrez Gene
SPOT_ID

Data table
ID SEQUENCE GC% Internal Repeat Score Self-Annealing Score Primary Strain Primary Target Common Name of Primary Target Gene Symbol Strain CO92 Strain KIM ORF SPOT_ID
3QYP00001_A_1 TGTTCAGAAAAGTTCAATACCTTCTGCGCTTGTTACTCCTTCCGTGCAACATAAGTGCGGGAAGGTGTGA 45.71 29 102 CO92 YPCD1.78c repA translation protein tap YPCD1.78c::70::100.0::7.0E-11::+ YKCD1p78::70::100.0::7.0E-11::+,Y0004::70::100.0::7.0E-11::+ YPCD1.78c
3QYP00001_A_10 TGCTTCAGTCCTCGATAGTAAAAGCAGCAGTGATGACTAAACCTTCAATTTTTGACATTAAAAACCACTT 35.71 29 71 KIM y0589 hypothetical protein y0589::70::100.0::3.7E-11::+ y0589
3QYP00001_A_11 AGTGCTGAAGTATCGCCTAACCTATTGAATCAGAATTTTAATCCACTGGGAATTAACCAGGTGTGGGTGA 41.43 29 85 CO92 YPMT1.77c possible transposase remnant YPMT1.77c::70::100.0::6.2E-11::+ Y1065::70::100.0::2.6E-11::+ YPMT1.77c
3QYP00001_A_12 CCAGACTGCAAGATTGTCCGTCGCCGTGGCCGAGTGTACGTAATTTGCAAAAGCAACCCTCGCTTTAAAG 51.43 29 82 CO92 YPO3135 50S ribosomal protein L36 YPO3135::70::100.0::3.6E-11::+ YPO3135
3QYP00001_A_13 ATTTATTGTTAATTTATCAACGTACCGACTCAGAAATTAAACTCTACCGTGTAGGAAGTCATTCTGATTT 31.43 29 88 KIM y0241 hypothetical protein y0241::70::100.0::6.2E-11::+ y0241
3QYP00001_A_14 TATACCTTTGGGTACAATAATAGCCTTGGGTACAATAATAATGTGCAAGTCTATCACTTTCTCCTGGACA 37.14 32 101 CO92 YPO3815 hypothetical protein YPO3815::70::100.0::3.6E-11::+ YPO3815
3QYP00001_A_15 GAATGAAGGGTTGACCGCACCTCGGGGCACTCCGGTGGCTTACGCCACTACGACCCCAACGGCACGTTTC 62.86 30 104 KIM y0374 hypothetical protein YPO0478::70::97.14286::2.1E-10::+ y0374::70::100.0::6.2E-11::+,y3696::70::97.14286::8.9E-11::-,y2176::70::97.14286::4.0E-10::+ y0374
3QYP00001_A_16 GCCTGTAACCCATCACCGCTGGCGGTACCGGAACGACTTAACCTGAGCGGGTCGGTCGATTTTATGCACA 57.14 29 91 CO92 YPCD1.18c transposase fragment YPCD1.18c::70::100.0::3.6E-11::+,YPCD1.89::69::92.753624::2.7E-9::+ YKCD1p70::69::92.753624::2.7E-9::+,Y0087.2N::69::92.753624::2.7E-9::+ YPCD1.18c
3QYP00001_A_17 AACCCGTCTACTAAGCCTACTACTTAACGCATCTCTCTTGCGCGGTATGTTGGTGGACGGAAATCAGAAC 48.57 29 92 KIM y3643 leu operon leader peptide leuL y3643::70::100.0::6.2E-11::+ y3643
3QYP00001_A_18 TCTGGTGCATCATCTGCATCACTCGCTCAGGGCTAGCAATACTCAGGGGGGTTGGTGGGTTAGCGGTGTG 57.14 32 69 KIM y0494 hypothetical protein YPO3735::70::100.0::1.8E-11::- y0495::70::100.0::1.8E-11::-,y0494::70::100.0::3.6E-11::+ y0494
3QYP00001_A_19 AATAACCCGAATCACTTACTGGTCGTTGACTTTAAAGTCAGTAAGCTCATCGGAATTAATGAGCCTTATC 38.57 28 139 KIM y0121 hypothetical protein y0121::70::100.0::6.0E-11::+ y0121
3QYP00001_A_2 CATTACCTTCATATGCACCAAATCAATGACTTAGCTAATTCTGTGGATGTAGCTCACAAATATGACATTG 35.71 30 113 CO92 YPO1423 hypothetical protein YPO1423::70::100.0::3.7E-11::+ YPO1423
3QYP00001_A_20 ATATTGATACGGTGTATGGCGTCACAATCTTTACTGGTGGAGATCGTTCATACTCTACGGCAGATAATCT 41.43 29 96 KIM y1126 hypothetical protein y1126::70::100.0::3.6E-11::+ y1126
3QYP00001_A_21 TGTTTAATCCAGTGGCGATGCCACCGACCTTATTGCGACCTGGGGATAATGTGCGCTTTCTGCCGCTAAA 51.43 29 76 CO92 YPO2698 pseudo gene YPO2698::70::100.0::8.0E-12::+ y1274::70::100.0::6.0E-11::+ YPO2698
3QYP00001_A_22 CCTGCAAGGGCTGTGGGTGGTAAATGCGGGGTATACGCATGGGTTTGCTCTAAGTCCTGAAACGAAAATC 51.43 30 78 KIM y3319 hypothetical protein y3319::70::100.0::3.6E-11::+ y3319
3QYP00001_A_23 GGGAGATGTTCCGTCTGGAACAACTCGAAAAAATTGCCTGCGAAAAGTCAAAACACGAGGTGTCAGACGG 48.57 30 91 KIM y3398 hypothetical protein y3398::70::100.0::6.0E-11::+ y3398
3QYP00001_A_24 TGCCAGAAAAATATCGATAATATGGTTAAATTTTCTAAAGATTTGCCTATCAACCTCATAAAAAATCCGC 30.0 31 91 CO92 YPO0571 hypothetical protein YPO0571::70::100.0::3.6E-11::+ y3608::70::100.0::3.6E-11::+ YPO0571
3QYP00001_A_3 GGACTGGATACAAGATAACAGCGAGATGTATCTGGCGGGAGACTGGCTCACACAAACGGGCTTAACTGGG 52.86 32 77 KIM y0253 hypothetical protein y0253::70::100.0::7.0E-11::+ y0253
3QYP00001_A_4 TTAAGCAAAAAAGGCTGAGGAGCGACTCCCCGGCAAAATGGTATTGTGGTGCTCAGAATGCAGTAAATAG 45.71 30 76 CO92 YPO1585 hypothetical protein YPO1585::70::100.0::3.7E-11::+ YPO1585
3QYP00001_A_5 GGTCATGCAAAAACGCGACCCAAAACAGGCGCGTCTCGTTATGGAAGCTACCGGTATTTATCATGAAGAT 47.14 29 118 CO92 YPO2314 putative invertase protein (partial) YPO2314::70::100.0::2.5E-11::+ y2018::70::100.0::7.0E-11::+ YPO2314

Total number of rows: 5329

Table truncated, full table size 1074 Kbytes.




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