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Platform GPL5870 Query DataSets for GPL5870
Status Public on Dec 13, 2007
Title JCVI PFGRC Salmonella typhimurium 25K v5 array designed primarily based on strain Ty2
Technology type spotted oligonucleotide
Distribution non-commercial
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Manufacturer JCVI PFGRC
Manufacture protocol 5QST, 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 5459 oligonucleotides, has 25392 spots distributed in 48 blocks.
 
Web link http://pfgrc.jcvi.org/descriptionPages.shtml
Submission date Sep 14, 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 CT18 Target map of strain CT18
Strain Ty2 Target map of strain Ty2
Strain LT2 (SGSC1412) Target map of strain LT2 (SGSC1412)
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 CT18 Strain Ty2 Strain LT2 (SGSC1412) ORF SPOT_ID
5QST00001_A_1 ATGAATTTAGTTAAAATTATTTATGAATTAAAACTCCCTAAACGTTTCCTCCAGAAAAATAAATACATTT 21.43 32 118 Ty2 t2592 hypothetical protein STY0293::70::100.0::1.1E-10::+ t2592::70::100.0::1.1E-10::+ t2592
5QST00001_A_10 ATACTATCGATCTTGGCAACAACGAATCTCTGGTATGTGGCGTGTTTCCCAATCAGGACGGCACATTCAC 47.14 29 78 CT18 STY2067 conserved hypothetical protein STY2067::70::100.0::5.1E-11::+ STY2067
5QST00001_A_11 TAACCGGCATCGTGCTGGTTTTCTTACTTTTAGGTTATCTGGTCTATGCCCTGATTAATGCGGAGGCGTT 45.71 29 78 LT2 (SGSC1412) STM0707 putative outer membrane protein STM0707::70::100.0::8.9E-11::+ STM0707
5QST00001_A_12 CGCCAGCAGCTTGATGCCGGGCGGATGACCACCACAAATTTTGCAGACGGCGACAGCGTAAAAGATAAAA 52.86 29 67 Ty2 t4506 hypothetical protein STY4810::70::100.0::5.1E-11::+ t4506::70::100.0::5.1E-11::+ t4506
5QST00001_A_13 TATTTACTGTGGTTTGTCGGCATTCTGCTGATGTGCTCACTGTCGACACTGGCGCTGGTATGGCTTGAGT 50.0 32 81 LT2 (SGSC1412) STM1794 putative periplasmic protein STM1794::70::100.0::8.9E-11::+ STM1794
5QST00001_A_14 TTCTGTGGGCCGTTTTACTCATCGTCACTATTTTATCATTCATTCATCATATGACCAATTCGCTGACTTT 37.14 30 78 LT2 (SGSC1412) STM1863 putative inner membrane protein STY2001::70::95.71428::8.3E-10::+ t1015::70::95.71428::8.3E-10::+ STM1863::70::100.0::5.0E-11::+ STM1863
5QST00001_A_15 TCACCATTCTTATCCTGAAACTCATTGTTGCAGCACTGCAACTGCTTGATGCTGTTCTGAAATACCTTAA 40.0 30 88 LT2 (SGSC1412) STM3796B conserved protein in the LexA regulon ysdB STM3796B::70::100.0::8.9E-11::+ STM3796B
5QST00001_A_16 AACACCCTTCTCTATCTCAACGGCTCGCAACTGGCGCGCAAAGAAAAGGAATATTGTTCCAGGCAGTGCG 51.43 30 74 LT2 (SGSC1412) STM2630 Gifsy-1 prophage STM2630::70::100.0::5.0E-11::+ STM2630
5QST00001_A_17 ATTGTCACCACTGCTCAATACTATGGCATAAAAACCGAAGAAAACGGTACTGTTCACTGTCTCGTTTCAT 40.0 30 73 Ty2 t1125 hypothetical protein STY1874a::70::100.0::8.9E-11::+ t1125::70::100.0::8.9E-11::+ t1125
5QST00001_A_18 TTATCCTTAATATCCTGCTGACATTACTCGGATATATTCCGGGGCTTATCCACGCATTTTGGGTTCAGAT 41.43 31 87 LT2 (SGSC1412) STM2796 putative YqaE family transport protein yqaE STY2916::70::98.57143::1.3E-10::+ t2691::70::98.57143::1.3E-10::+ STM2796::70::100.0::5.0E-11::+ STM2796
5QST00001_A_19 ATTCCTGTTTACTGACGAAAAGTGCGCCAGAAAAGCGTATTATAATTTATCCATCACTGACATATGTGAT 35.71 30 75 Ty2 t1124 hypothetical protein STY1874b::70::100.0::8.9E-11::+ t1124::70::100.0::8.9E-11::+ t1124
5QST00001_A_2 TTGATGGTTCAGTAATTGGTATGTGCGCGCTACCCAACGGCAAACGTTGTAGCGAACAGTCGCTTGCCGC 52.86 30 94 Ty2 t1552 hypothetical protein STY1420::70::100.0::5.1E-11::+ t1552::70::100.0::5.1E-11::+ STM1649::70::100.0::5.1E-11::+ t1552
5QST00001_A_20 ACACAATAGTGGGTTTCACTGGCAGCACACAATCAAATCTGACAGTCGGCTTCGAGCGAGGTGCGGACAT 51.43 31 80 Ty2 t0348 hypothetical protein STY2750::70::100.0::5.0E-11::+ t0348::70::100.0::5.0E-11::+ t0348
5QST00001_A_21 CTATATTCCTCACGCGCCAGCAAAATCTGGCGTCGGGATTGGCGTCCCGGATGTTTACGGAGCGATATGA 54.29 28 108 CT18 STY2049 hypothetical protein STY2049::70::100.0::8.3E-11::+ STY2049
5QST00001_A_22 AGTCTGGCTTGACGAGTTCTGCTATTGCAACATGGAGCAACAGCGCACACAGCCTGAAGGCCGTGGCTAA 54.29 28 111 LT2 (SGSC1412) STM0436A IS903 transposase STM0436A::70::100.0::4.9E-11::+ STM0436A
5QST00001_A_23 TGAACCCTTCCATGCTGAACGCGACCCTACTAACAACTGCGCCATCTCGCGCAGTGGTCGTCGTGCGTGT 58.57 30 111 Ty2 t3721 ilvBN operon attenuator peptide ivbL STY3985::70::100.0::8.1E-11::+ t3721::70::100.0::8.1E-11::+ STM3797::70::100.0::8.1E-11::+ t3721
5QST00001_A_24 AATCTGGCCTCCAGGCTGGCTTAAATATGCGCACATGACAATACAACCGGAAAATTTACAAAACCCATAA 41.43 30 77 LT2 (SGSC1412) STM1999 putative cytoplasmic protein STY2207::70::95.71428::8.2E-10::+ t0879::70::95.71428::8.2E-10::+ STM1999::70::100.0::4.9E-11::+ STM1999
5QST00001_A_3 ATGAGCTTACAGGAGTTGTTTGAGCTCGTCCTCTGTGTCCACTTGGTCTGCCAGATGCTCTACAGGGAGT 51.43 32 72 Ty2 t2947 hypothetical protein t2947::70::100.0::1.1E-10::+ t2947
5QST00001_A_4 TTTATTTTGTGGGTAACCCCTCCGCTTTTTGATCAAAAAACAACCACTGCTATTTTTAGCGTAGCTTATG 37.14 30 102 LT2 (SGSC1412) STM1948 putative inner membrane protein STY2156::70::98.57143::1.3E-10::+ t0928::70::98.57143::1.3E-10::+ STM1948::70::100.0::5.1E-11::+ STM1948
5QST00001_A_5 ATGCTCAGAAAATTTCAATACTTGTTTCTGTGGCATTTACTCCTTCCGTGCATTGTAAGTGCAGGCAGAA 40.0 29 86 LT2 (SGSC1412) PSLT005 replication of plasmid tap PSLT005::70::100.0::1.0E-10::+ PSLT005

Total number of rows: 5972

Table truncated, full table size 1385 Kbytes.




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