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Platform GPL8969 Query DataSets for GPL8969
Status Public on Aug 04, 2009
Title JCVI PFGRC Yersinia pestis 19K v4 array designed primarily based on strain PB1/+
Technology type spotted oligonucleotide
Distribution non-commercial
Organism Yersinia pestis
Manufacturer JCVI PFGRC
Manufacture protocol 4QYP, with arrayer GENETIX, 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 19200 spots distributed in 48 blocks.
 
Web link http://pfgrc.jcvi.org/descriptionPages.shtml
Submission date Jul 31, 2009
Last update date Aug 04, 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
 

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
4QYP00001_A_1 TGTTCAGAAAAGTTCAATACCTTCTGCGCTTGTTACTCCTTCCGTGCAACATAAGTGCGGGAAGGTGTGA 45.71 29 102 91001 YP_pCD07 putative 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::+ YP_pCD07
4QYP00001_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
4QYP00001_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
4QYP00001_A_12 CCAGACTGCAAGATTGTCCGTCGCCGTGGCCGAGTGTACGTAATTTGCAAAAGCAACCCTCGCTTTAAAG 51.43 29 82 PB1/+ YPTS_1023 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::+ YPTS_1023
4QYP00001_A_13 ATTTATTGTTAATTTATCAACGTACCGACTCAGAAATTAAACTCTACCGTGTAGGAAGTCATTCTGATTT 31.43 29 88 KIM y0241 hypothetical protein y0241::70::100.0::2.1E-10::+ y0241
4QYP00001_A_14 TATACCTTTGGGTACAATAATAGCCTTGGGTACAATAATAATGTGCAAGTCTATCACTTTCTCCTGGACA 37.14 32 101 91001 YP_3234 hypothetical protein YPO3815::70::100.0::1.2E-10::+ YP_3234::70::100.0::1.2E-10::+ YP_3234
4QYP00001_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
4QYP00001_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
4QYP00001_A_17 AACCCGTCTACTAAGCCTACTACTTAACGCATCTCTCTTGCGCGGTATGTTGGTGGACGGAAATCAGAAC 48.57 29 92 KIM y3643 leu operon leader peptide leuL y3643::70::100.0::2.1E-10::+ y3643
4QYP00001_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
4QYP00001_A_19 AATAACCCGAATCACTTACTGGTCGTTGACTTTAAAGTCAGTAAGCTCATCGGAATTAATGAGCCTTATC 38.57 28 139 KIM y0121 hypothetical protein y0121::70::100.0::2.0E-10::+ y0121
4QYP00001_A_2 CATTACCTTCATATGCACCAAATCAATGACTTAGCTAATTCTGTGGATGTAGCTCACAAATATGACATTG 35.71 30 113 91001 YP_1170 hypothetical protein YPO1423::70::100.0::1.2E-10::+ YP_1170::70::100.0::1.2E-10::+ YP_1170
4QYP00001_A_20 ATATTGATACGGTGTATGGCGTCACAATCTTTACTGGTGGAGATCGTTCATACTCTACGGCAGATAATCT 41.43 29 96 PB1/+ YPTS_1102 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::+ YPTS_1102
4QYP00001_A_21 TGTTTAATCCAGTGGCGATGCCACCGACCTTATTGCGACCTGGGGATAATGTGCGCTTTCTGCCGCTAAA 51.43 29 76 PB1/+ YPTS_3023 allophanate hydrolase subunit 1 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::+ YPTS_3023
4QYP00001_A_22 CCTGCAAGGGCTGTGGGTGGTAAATGCGGGGTATACGCATGGGTTTGCTCTAAGTCCTGAAACGAAAATC 51.43 30 78 KIM y3319 hypothetical protein y3319::70::100.0::1.2E-10::+ y3319
4QYP00001_A_23 GGGAGATGTTCCGTCTGGAACAACTCGAAAAAATTGCCTGCGAAAAGTCAAAACACGAGGTGTCAGACGG 48.57 30 91 KIM y3398 hypothetical protein y3398::70::100.0::2.0E-10::+ y3398
4QYP00001_A_24 TGCCAGAAAAATATCGATAATATGGTTAAATTTTCTAAAGATTTGCCTATCAACCTCATAAAAAATCCGC 30.0 31 91 91001 YP_2891 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::+ YP_2891
4QYP00001_A_3 GGACTGGATACAAGATAACAGCGAGATGTATCTGGCGGGAGACTGGCTCACACAAACGGGCTTAACTGGG 52.86 32 77 KIM y0253 hypothetical protein y0253::70::100.0::2.3E-10::+ y0253
4QYP00001_A_4 TTAAGCAAAAAAGGCTGAGGAGCGACTCCCCGGCAAAATGGTATTGTGGTGCTCAGAATGCAGTAAATAG 45.71 30 76 CO92 YPO1585 hypothetical protein YPO1585::70::100.0::1.2E-10::+ YPO1585
4QYP00001_A_5 GGTCATGCAAAAACGCGACCCAAAACAGGCGCGTCTCGTTATGGAAGCTACCGGTATTTATCATGAAGAT 47.14 29 118 91001 YP_2101 len: 52 aa, Best Blastp hit 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::+ YP_2101

Total number of rows: 8141

Table truncated, full table size 2858 Kbytes.




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Supplementary data files not provided
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