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Platform GPL9009 Query DataSets for GPL9009
Status Public on Aug 13, 2009
Title JCVI PFGRC Yersinia pestis 18K v5 array designed primarily based on strain CO92
Technology type spotted oligonucleotide
Distribution non-commercial
Organism Yersinia pestis CO92
Manufacturer JCVI PFGRC
Manufacture protocol 5QYP, with arrayer AUSHON, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000
Coating aminosilane
 
Description This set includes 7359 oligonucleotides, has 18240 spots distributed in 48 blocks.
 
Web link http://pfgrc.jcvi.org/descriptionPages.shtml
Submission date Aug 10, 2009
Last update date Aug 13, 2009
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
 
Samples (54) GSM723034, GSM723035, GSM723036, GSM723037, GSM723038, GSM723039 
Series (7)
GSE29240 Yersinia pestis uses AHL-based quorum sensing to regulate metabolic functions likely to be important for flea colonization
GSE30328 Global gene expression analysis of Yersinia pestis Ysp AHL quorum sensing at 37°C
GSE30329 Global gene expression analysis of Yersinia pestis Ysp AHL quorum sensing at 30°C

Data table header descriptions
ID Unique identification of each oligo
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
Strain 91001 Target map of strain 91001
Strain Nepal516 Target map of strain Nepal516
Strain Antiqua Target map of strain Antiqua
Strain Pestoides_F Target map of strain Pestoides_F
Strain PB1/+ Target map of strain PB1/+
ORF
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 Strain 91001 Strain Nepal516 Strain Antiqua Strain Pestoides_F Strain PB1/+ ORF SPOT_ID
5QYP00001_A_1 TGTTCAGAAAAGTTCAATACCTTCTGCGCTTGTTACTCCTTCCGTGCAACATAAGTGCGGGAAGGTGTGA 45.71 29 102 CO92 YPCD1.78c repA translation protein tap YPCD1.78c::70::100.0::2.3E-10::+ Y0004::70::100.0::2.3E-10::+ YP_pCD07::70::100.0::2.3E-10::+ YPCD1.78c
5QYP00001_A_10 TGCTTCAGTCCTCGATAGTAAAAGCAGCAGTGATGACTAAACCTTCAATTTTTGACATTAAAAACCACTT 35.71 29 71 Antiqua YPA_3951 hypothetical protein y0589::70::100.0::1.2E-10::+ YPN_3339::70::100.0::1.2E-10::+ YPA_3951::70::100.0::1.2E-10::+ YPDSF_3641::70::100.0::1.4E-10::+ YPA_3951
5QYP00001_A_11 AGTGCTGAAGTATCGCCTAACCTATTGAATCAGAATTTTAATCCACTGGGAATTAACCAGGTGTGGGTGA 41.43 29 85 91001 YP_pMT123 transposase YP_pMT123::70::100.0::8.8E-11::+ YPA_MT0097::70::100.0::8.8E-11::+ YPDSF_4157::70::100.0::8.8E-11::+ YP_pMT123
5QYP00001_A_12 CCAGACTGCAAGATTGTCCGTCGCCGTGGCCGAGTGTACGTAATTTGCAAAAGCAACCCTCGCTTTAAAG 51.43 29 82 CO92 YPO3135 50S ribosomal protein L36 rpmJ YPO3135::70::100.0::1.2E-10::+ YP_0796::70::100.0::1.2E-10::+ YPN_0955::70::100.0::1.2E-10::+ YPA_2630::70::100.0::1.2E-10::+ YPDSF_2770::70::100.0::1.2E-10::+ YPTS_1023::70::100.0::1.2E-10::+ YPO3135
5QYP00001_A_13 ATTTATTGTTAATTTATCAACGTACCGACTCAGAAATTAAACTCTACCGTGTAGGAAGTCATTCTGATTT 31.43 29 88 KIM y0241 hypothetical protein y0241::70::100.0::2.1E-10::+ y0241
5QYP00001_A_14 TATACCTTTGGGTACAATAATAGCCTTGGGTACAATAATAATGTGCAAGTCTATCACTTTCTCCTGGACA 37.14 32 101 CO92 YPO3815 hypothetical protein YPO3815::70::100.0::1.2E-10::+ YP_3234::70::100.0::1.2E-10::+ YPO3815
5QYP00001_A_15 GAATGAAGGGTTGACCGCACCTCGGGGCACTCCGGTGGCTTACGCCACTACGACCCCAACGGCACGTTTC 62.86 30 104 KIM y0374 hypothetical protein YPO0478::70::97.14286::6.9E-10::+ y0374::70::100.0::2.1E-10::+,y3696::70::97.14286::3.0E-10::-,y2176::70::97.14286::1.4E-9::+ YP_3701::70::97.14286::6.9E-10::+ YPN_0351::70::97.14286::6.9E-10::+ y0374
5QYP00001_A_16 GCCTGTAACCCATCACCGCTGGCGGTACCGGAACGACTTAACCTGAGCGGGTCGGTCGATTTTATGCACA 57.14 29 91 91001 YP_pCD69 possible transposase remnant, len: 81 aa, Best Blastp hit YP_pCD69::70::100.0::7.2E-11::+,YP_pCD94::69::92.753624::8.4E-9::+ YPA_CD0043::70::100.0::7.3E-11::+,YPA_CD0060::69::92.753624::8.4E-9::+ YPDSF_4002::70::100.0::7.3E-11::+,YPDSF_4023::69::92.753624::8.4E-9::+ YPTS_4239::69::92.753624::8.4E-9::+ YP_pCD69
5QYP00001_A_17 AACCCGTCTACTAAGCCTACTACTTAACGCATCTCTCTTGCGCGGTATGTTGGTGGACGGAAATCAGAAC 48.57 29 92 KIM y3643 leu operon leader peptide leuL y3643::70::100.0::2.1E-10::+ y3643
5QYP00001_A_18 TCTGGTGCATCATCTGCATCACTCGCTCAGGGCTAGCAATACTCAGGGGGGTTGGTGGGTTAGCGGTGTG 57.14 32 69 KIM y0494 hypothetical protein YPO3735::70::100.0::6.1E-11::- y0495::70::100.0::6.1E-11::-,y0494::70::100.0::1.2E-10::+ YP_3098::70::100.0::6.1E-11::- YPN_0230::70::100.0::4.9E-11::- YPA_3608::70::100.0::4.9E-11::- YPDSF_3733::70::100.0::4.9E-11::- YPTS_0314::70::100.0::6.1E-11::- y0494
5QYP00001_A_19 AATAACCCGAATCACTTACTGGTCGTTGACTTTAAAGTCAGTAAGCTCATCGGAATTAATGAGCCTTATC 38.57 28 139 KIM y0121 hypothetical protein y0121::70::100.0::2.0E-10::+ y0121
5QYP00001_A_2 CATTACCTTCATATGCACCAAATCAATGACTTAGCTAATTCTGTGGATGTAGCTCACAAATATGACATTG 35.71 30 113 CO92 YPO1423 hypothetical protein YPO1423::70::100.0::1.2E-10::+ YP_1170::70::100.0::1.2E-10::+ YPO1423
5QYP00001_A_20 ATATTGATACGGTGTATGGCGTCACAATCTTTACTGGTGGAGATCGTTCATACTCTACGGCAGATAATCT 41.43 29 96 Antiqua YPA_2550 hypothetical protein y1126::70::100.0::1.2E-10::+ YPN_1036::70::100.0::1.2E-10::+ YPA_2550::70::100.0::1.2E-10::+ YPDSF_2694::70::100.0::1.4E-10::+ YPTS_1102::70::100.0::1.4E-10::+ YPA_2550
5QYP00001_A_21 TGTTTAATCCAGTGGCGATGCCACCGACCTTATTGCGACCTGGGGATAATGTGCGCTTTCTGCCGCTAAA 51.43 29 76 CO92 YPO2698 pseudo YPO2698::70::100.0::2.7E-11::+ y1274::70::100.0::2.0E-10::+ YP_2502::70::100.0::2.7E-11::+ YPTS_3023::70::100.0::2.7E-11::+ YPO2698
5QYP00001_A_22 CCTGCAAGGGCTGTGGGTGGTAAATGCGGGGTATACGCATGGGTTTGCTCTAAGTCCTGAAACGAAAATC 51.43 30 78 KIM y3319 hypothetical protein y3319::70::100.0::1.2E-10::+ y3319
5QYP00001_A_23 GGGAGATGTTCCGTCTGGAACAACTCGAAAAAATTGCCTGCGAAAAGTCAAAACACGAGGTGTCAGACGG 48.57 30 91 KIM y3398 hypothetical protein y3398::70::100.0::2.0E-10::+ y3398
5QYP00001_A_24 TGCCAGAAAAATATCGATAATATGGTTAAATTTTCTAAAGATTTGCCTATCAACCTCATAAAAAATCCGC 30.0 31 91 CO92 YPO0571 hypothetical protein YPO0571::70::100.0::1.2E-10::+ y3608::70::100.0::1.2E-10::+ YP_2891::70::100.0::1.2E-10::+ YPN_0440::70::100.0::1.2E-10::+ YPA_3217::70::100.0::1.2E-10::+ YPDSF_0358::70::98.57143::3.1E-10::+ YPO0571
5QYP00001_A_3 GGACTGGATACAAGATAACAGCGAGATGTATCTGGCGGGAGACTGGCTCACACAAACGGGCTTAACTGGG 52.86 32 77 KIM y0253 hypothetical protein y0253::70::100.0::2.3E-10::+ y0253
5QYP00001_A_4 TTAAGCAAAAAAGGCTGAGGAGCGACTCCCCGGCAAAATGGTATTGTGGTGCTCAGAATGCAGTAAATAG 45.71 30 76 CO92 YPO1585 hypothetical protein YPO1585::70::100.0::1.2E-10::+ YPO1585
5QYP00001_A_5 GGTCATGCAAAAACGCGACCCAAAACAGGCGCGTCTCGTTATGGAAGCTACCGGTATTTATCATGAAGAT 47.14 29 118 CO92 YPO2314 putative invertase protein (partial) YPO2314::70::100.0::8.5E-11::+ y2018::70::100.0::2.3E-10::+ YP_2101::70::100.0::1.1E-10::+ YPN_1776::70::100.0::1.1E-10::+ YPA_1662::70::100.0::1.1E-10::+ YPDSF_0830::70::100.0::1.1E-10::+ YPO2314

Total number of rows: 8141

Table truncated, full table size 2814 Kbytes.




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Supplementary data files not provided
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