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Platform GPL14855 Query DataSets for GPL14855
Status Public on Dec 06, 2011
Title NIMBLE_MMCCSAL07_14028_380k [MMCCSAL07_100416_SP_CGH]
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
Manufacturer Roche (NimbleGen, Inc.)
Manufacture protocol in situ oligonucleotide
 
Description design name: MMCCSAL07_100416_SP_CGH
This set includes 374328 46~50mer oligonucleotides that hit both Typhimurium LT2 and Typhimurium 14028s, complemented with 10451 oligos that are specific for 14028s (and 100 duplicate spots). The probes were designed based on the Salmonella typhimurium LT2 (NC_003197.1) and 14028s (CP001363.1: complete genome and CP001362.1: plasmid) genomes, with a moving window of about 12 bases. All probes (including control oligos) are represented in this file.
 
Contributor(s) Long F, McClelland M, Porwollik S
Submission date Nov 07, 2011
Last update date Sep 18, 2013
Contact name Michael McClelland
E-mail(s) mcclelland.michael@gmail.com
Phone 858-336-9554
Organization name University of California, Irvine
Department Microbiology & Molecular Genetics
Street address 132 Med Surge I
City Irvine
State/province CA
ZIP/Postal code 92697
Country USA
 
Samples (34) GSM829445, GSM829446, GSM829447, GSM829448, GSM829449, GSM829450 
Series (8)
GSE33529 Role of DksA in nitrosative stress
GSE34134 Role of the ArcAB two-component system in oxidative stress
GSE47165 Identification of Salmonella genes regulated by STM2239

Data table header descriptions
ID
BLOCK Array Block
ROW_NUM Array Row
COL_NUM Array Column
PROBE_NAME Name of Oligo
SEQUENCE oligo Sequence
14028_HIT_COUNT_95PC Number of hits >95%ID in genome of ATCC14028
14028_PCID_BEST_HIT %ID of best hit in genome of ATCC14028
CHROMOSOME ATCC14028 (14028s) or plasmid (14028s_plasmid)
STRAND Strand of Oligo match in the ATCC14028 genome
RANGE_GB ACCESSION.VERSION
RANGE_START 5' Oligo position in the ATCC14028 genome
RANGE_END 3' Oligo position in the ATCC14028 genome
GENE_ID ATCC14028 gene number according to MMCC annotation 100728; locus tag STM14_*
GENE_NAME ATCC14028 gene name according to MMCC annotation 100728
PROBE_DESIGN_ID
X
Y

Data table
ID BLOCK ROW_NUM COL_NUM PROBE_NAME SEQUENCE 14028_HIT_COUNT_95PC 14028_PCID_BEST_HIT CHROMOSOME STRAND RANGE_GB RANGE_START RANGE_END GENE_ID GENE_NAME PROBE_DESIGN_ID X Y
MMCCSAL07_00001 1 1 1 SalmP276599 GGTAAACGTGGTGGTGCCGATGGGCTATCCGGCCAATAACCAGGACTATA 1 100 14028S + CP001363.1 4150368 4150417 STM14_4725 wecF [D] 11865_0001_0001 1 1
MMCCSAL07_00002 1 3 1 SalmP221424 GCATCCCGTTTGCGTCAGTTGCATGAATTTTCGATTATTGATCTTGATGA 1 100 14028S - CP001363.1 933178 933227 STM14_1008 gltC [J] 11865_0001_0003 1 3
MMCCSAL07_00003 1 5 1 SalmP227374 GCCCTGTTTGAACGTCTGGGCTGGAAAGTGTCGCTCAAGCGTCTGAAT 1 100 14028S - CP001363.1 3329416 3329463 STM14_3812 hybB 11865_0001_0005 1 5
MMCCSAL07_00004 1 7 1 SalmP103074 CATATAGATTGCATGGCTCTCCATCTTTCCCATACTGTACAAGATAAAAA 1 100 14028S - CP001363.1 2913701 2913750 STM14_3319 11865_0001_0007 1 7
MMCCSAL07_00005 1 9 1 SalmP272926 GGGCAGGCGAATCGCACAAGCGTCGATCTGTCGACATTTGATAACGACAA 1 100 14028S - CP001363.1 208155 208204 STM14_0207 stiC 11865_0001_0009 1 9
MMCCSAL07_00006 1 11 1 SalmP137509 CCTGTTCGTTAAAGCAGGCGGCGCTGCCGTTGATACGTGATGTGAG 1 100 14028S - CP001363.1 1804641 1804686 STM14_2055 yciW 11865_0001_0011 1 11
MMCCSAL07_00007 1 13 1 SalmP231675 GCCTGCCGGAAATTCTGGTGGTGCTGTTTATCTATTTCGGCTCCTCGCAA 1 100 14028S - CP001363.1 961124 961173 STM14_1041 artQ 11865_0001_0013 1 13
MMCCSAL07_00008 1 15 1 SalmP061992 AGGGTACGCACCGATAATATAACCGGTATTATTTTTCATTTTGTGCTCCA 1 100 14028S - CP001363.1 3870817 3870866 STM14_4427 11865_0001_0015 1 15
MMCCSAL07_00009 1 17 1 SalmP094288 CACTTTTTGCTCAGGCAATGCGCCATAAAAGCCCCTGACTTCAGCGC 1 100 14028S - CP001363.1 4797984 4798030 STM14_5439 mrr 11865_0001_0017 1 17
MMCCSAL07_00010 1 19 1 SalmP183000 CTCCGCCGTGGTCATGGGCGGTCTGGCGATCGCGCGGGTTCCCTATGTCC 1 100 14028S - CP001363.1 4718723 4718772 STM14_5357 arcD [R] 11865_0001_0019 1 19
MMCCSAL07_00011 1 21 1 SalmP277113 GGTAATGGCCATACAGGCCATGATCATGTCAGCGAGCTGCCATATCAGCG 1 100 14028S + CP001363.1 6131 6180 STM14_0006.R yaaJ 11865_0001_0021 1 21
MMCCSAL07_00012 1 23 1 SalmP225768 GCCATTCGCTGGCATTTGAAATTGCCGACGTTTGCCCTGGATGAAAACG 1 100 14028S - CP001363.1 241321 241369 STM14_0245 yadS 11865_0001_0023 1 23
MMCCSAL07_00013 1 25 1 SalmP087656 CAAGCCAGTGCTGCGGCGCGCCATGAGGACTTCCTGCAACAGTAGACGCG 1 100 14028S - CP001363.1 3682874 3682923 STM14_4227 gntX [D] 11865_0001_0025 1 25
MMCCSAL07_00014 1 27 1 SalmP292767 GTCTCTGGCATGCGCCGTAAAACCTGAGGTGGTAATAAAGACGCCACGT 1 100 14028S - CP001363.1 4798033 4798081 STM14_5439 mrr 11865_0001_0027 1 27
MMCCSAL07_00015 1 29 1 SalmP044208 ACTTACCAGTTATAGCGCAGATTGAGGCTACCGTTCAGATCGCCAAAGTC 1 100 14028S + CP001363.1 2679140 2679189 STM14_3078.LJ shdA 11865_0001_0029 1 29
MMCCSAL07_00016 1 31 1 SalmP286725 GTAGATTCTGCTGCTGATAATGGACTATTAACCCCTGTAGAAACCACGGT 1 100 14028S + CP001363.1 2945919 2945968 STM14_3348 iroN 11865_0001_0031 1 31
MMCCSAL07_00017 1 33 1 SalmP303456 GTTTGCTTCAGCGCGCTCACGCCCGGTAATGTCACCAGCGTATTGATCTG 1 100 14028S + CP001363.1 3522409 3522458 STM14_4030 nanA 11865_0001_0033 1 33
MMCCSAL07_00018 1 35 1 SalmP324365 TCCCCATCCTGCGGTAATAAACAGAACTGGCATTAAAATACGCGCTATCA 1 100 14028S - CP001363.1 3416319 3416368 STM14_3914 yqjF 11865_0001_0035 1 35
MMCCSAL07_00019 1 37 1 SalmP117223 CCATGGCGGTTAGCATATCGGTCTTGTACAGGCCATCTGCGGTTAAGCC 1 100 14028S + CP001363.1 4635964 4636012 STM14_5263 ulaR [D] 11865_0001_0037 1 37
MMCCSAL07_00020 1 39 1 SalmP335381 TCTCTTTTATCGGTTCAAACACGCCTGACGACCCCGGCAGCATGTTCT 1 100 14028S + CP001363.1 3004568 3004615 STM14_3430 fhlA [J] 11865_0001_0039 1 39

Total number of rows: 392936

Table truncated, full table size 65294 Kbytes.




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Supplementary file Size Download File type/resource
GPL14855_MMCCSAL07_100416_SP_CGH.ndf.gz 13.8 Mb (ftp)(http) NDF

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