| 1 |
GPL16797 |
Custom NimbleGen Shewanella oneidensis MR-1 Tiling v2 [NimbleGen_MR1_2005K_1] |
2,023,636 |
University of California |
2013-03-15 |
NimbleGen |
Shewanella oneidensis MR-1
 |
Tiling Array |
in situ oligonucleotide, Custom NimbleGen Shewanella oneidensis MR-1 Tiling v2 [NimbleGen_MR1_2005K_1], NC_004347 and NC_004349 100318_Shew_one_MR1_JK_EXP_HX1.ndf |
| 2 |
GPL13654 |
NimbleGen Desulfovibrio vulgaris Hildenborough 2004K |
2,003,627 |
Lawrence Berkeley Lab |
2011-05-26 |
NimbleGen |
Desulfovibrio vulgaris str. Hildenborough
 |
Oligo Array |
in situ oligonucleotide, NimbleGen Desulfovibrio vulgaris Hildenborough 2004K, |
| 3 |
GPL15823 |
Custom NimbleGen Shewanella oneidensis MR-1 Tiling [NimbleGen_MR1_2005K_1] |
1,937,190 |
Lawrence Berkeley Lab |
2012-07-18 |
NimbleGen |
Shewanella oneidensis MR-1
|
Tiling Array |
in situ oligonucleotide, Custom NimbleGen Shewanella oneidensis MR-1 Tiling [NimbleGen_MR1_2005K_1], NC_004347 and NC_004349 100318_Shew_one_MR1_JK_EXP_HX1.ndf |
| 4 |
GPL11655 |
NimbleGen Clostridium_thermocellum_ATCC27405_Tiling_3Plex |
631,460 |
National Renewable Energy Lab |
2011-01-26 |
NimbleGen |
Clostridium thermocellum ATCC 27405
 |
Oligo Array |
in situ oligonucleotide, NimbleGen Clostridium_thermocellum_ATCC27405_Tiling_3Plex, Custom array. Design ID: 10425. DESIGN_NAME: 090803_Ctherm_SB_EXP SLIDE_LAYOUT_NAME: NimbleChip_HX3 The array is based on CP000568.1 |
| 5 |
GPL13535 |
Agilent Array ID 022715 (forward strand) and Array ID 022716 (reverse strand) |
458,333 |
Harvard University |
2011-05-15 |
Agilent |
Synechococcus elongatus PCC 7942
 |
Oligo Array |
in situ oligonucleotide, Agilent Array ID 022715 (forward strand) and Array ID 022716 (reverse strand), Agilent 1x244k |
| 6 |
GPL11291 |
Porphyromonas gingivalis W83 genomic tiling array mapped format |
409,807 |
The Forsyth Institute |
2010-12-07 |
Roche NimbleGen Inc. |
Porphyromonas gingivalis W83
 |
Tiling Array |
in situ oligonucleotide, Porphyromonas gingivalis W83 genomic tiling array mapped format, The probe set printed on the array consists of 380,000 unique oligonucleotide sequences. On this particular platform, all the 380k unique probes were mapped to all the matched loci of the reference genome, thus each unique probe sequence may appear multiple times due to the repeated probe sequence found in the genome. |
| 7 |
GPL14855 |
NIMBLE_MMCCSAL07_14028_380k [MMCCSAL07_100416_SP_CGH] |
392,936 |
Vaccine Research Institute of San Diego |
2011-11-07 |
Roche (NimbleGen, Inc.) |
Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
 |
Oligo Array |
in situ oligonucleotide, NIMBLE_MMCCSAL07_14028_380k [MMCCSAL07_100416_SP_CGH], 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. |
| 8 |
GPL11276 |
Genome Institute of Singapore Burkholderia pseudomallei 390K tiling array [2007-02-26_BpK96243_Yiting_FT] |
392,778 |
Genome Institute of Singapore |
2010-12-03 |
NimbleGen |
Burkholderia pseudomallei K96243
 |
Tiling Array |
in situ oligonucleotide, Genome Institute of Singapore Burkholderia pseudomallei 390K tiling array [2007-02-26_BpK96243_Yiting_FT], aCGH experiments were performed using oligonucleotide microarrays comprising > 390,000 50-mer probes providing tiling coverage of the Bp K96243 reference genome (15 bp overlap) (NimbleGen, Reykjavik, Iceland) |
| 9 |
GPL7369 |
Institute for Systems Biology NimbleGen Halobacterium 391k tiling array |
391,015 |
Institute for Systems Biology |
2008-09-24 |
Nimblegen |
Halobacterium sp. NRC-1
 |
Tiling Array |
in situ oligonucleotide, Institute for Systems Biology NimbleGen Halobacterium 391k tiling array, |
| 10 |
GPL15047 |
NIMBLE_MMCCSAL05_14028_380k |
389,480 |
Vaccine Research Institute of San Diego |
2011-12-21 |
Roche (NimbleGen, Inc.) |
Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
|
Oligo Array |
in situ oligonucleotide, NIMBLE_MMCCSAL05_14028_380k, design name: MMCCSAL05_081030. This set includes 374328 (of 374433) 46~50mer oligonucleotides that hit both Typhimurium LT2 and Typhimurium 14028s, complemented with 10576 oligos that are specific for 14028s, 894 (of 900) oligos that are specific for Enteritidis PT4, 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. The PT4-specific probes were designed based on genome NC_011294. All probes (including control oligos) are represented in this file. |
| 11 |
GPL7231 |
Lactococcus lactis pangenome 385K short oligo array |
389,479 |
CMBI |
2008-08-29 |
NimbleGen Systems Inc. (Madison, WI, USA) |
Lactococcus lactis
 |
Tiling Array |
in situ oligonucleotide, Lactococcus lactis pangenome 385K short oligo array, All genomic, plasmid and single gene or operon DNA sequences (1988 sequences in July 2005, constituting 10.7 Mb) of L. lactis were collected from the NCBI CoreNucleotide database and were deposited in a local database. This included complete genome sequences of L. lactis strain IL1403 (2.35 Mb, accession number AE005176) and fragments of the genome of strain SK11 (2.43 Mb, Genbank record GI:62464763). Additionally, draft genome sequences consisting of 547 contigs (2.3 Mb) of L. lactis ssp. lactis strain KF147 (NIZOB2230) and 961 contigs (2.6 Mb) of L. lactis ssp. lactis KF282 (NIZOB2244W) were added to this database. Redundant stretches of DNA were removed from the database, where a stretch of DNA was defined as redundant if it differed from another piece of DNA by at most 2 nucleotides over a window of 100 nucleotides. For the remaining non-redundant 7 Mb of DNA, a 32-mer tiling design was defined by starting an oligomer approximately every 19 nucleotides, resulting in a total of 386,298 probes. We also designed 3181 random probes with their sequence absent in the non-redundant 7 Mb of DNA and they were randomly located on the array. Probes target mainly L. lactis ssp. lactis IL1403 public genome and then incomplete genome of L. lactis ssp. cremoris SK11 (now it is completed). Recently, closely related genome of strain L. lactis ssp. cremoris MG1363 has been published. All these 3 genomes are publicly available at NCBI databases. Since there is no reference strain the probes target DNA from different strains, hence, there is no positions file (*.pos). The .ndf file is linked below as a supplementary file. |
| 12 |
GPL10416 |
NimbleGen E. coli K12 Mg1655 385K array |
389,307 |
National Yang-Ming University |
2010-05-15 |
NimbleGen |
Escherichia coli str. K-12 substr. MG1655
 |
Tiling Array |
in situ oligonucleotide, NimbleGen E. coli K12 Mg1655 385K array, This is a commercial 385K high density tiling array from NimbleGen for E. coli K12 MG1655 (Cat. No. 05542901001). The design contains 50-mer probe with 24 bp median probe spacing and the control probes are also included. native array description file: 2006-07-18_Ecoli_K12_ChIP.ndf native array description file: 2006-07-18_Ecoli_K12_ChIP.pos |
| 13 |
GPL10653 |
Sf301_Nimblegen_380k array |
389,307 |
Chinese center for disease control and prevention |
2010-07-07 |
NimbleGen |
Shigella flexneri 2a str. 301
 |
Oligo Array |
in situ oligonucleotide, Sf301_Nimblegen_380k array, NimbleGen design name 2007-02-12_CSB_Sflexneri_tiling, design for Shigella flexneri 2a strain 301 and associated plasmid pCP301. The design includes random GC and other control probes. The .ndf file is linked below as a supplementary file. |
| 14 |
GPL13947 |
Nimblegen Salmonella Typhimurium LT2 TI99287 60mer |
389,307 |
University of Wisconsin-Madison |
2011-07-19 |
NimbleGen |
Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
|
Oligo Array |
in situ oligonucleotide, Nimblegen Salmonella Typhimurium LT2 TI99287 60mer, Catalog design for Salmonella typhimurium LT2 (Taxonomy Id: 99287) covering NC_003197, NC_003277. Probes selected for 4527/4527 sequences. Median number of probes/sequence is 17 with an average of 17.00. Each probe will be replicated 5 times on the chip. Probes are randomly distributed over the surface of the array. Unused features have been filled with randomly generated probes of comparable GC content. |
| 15 |
GPL5728 |
NIMBLE_MMCCSAL01_380k |
386,350 |
Vaccine Research Institute of San Diego |
2007-08-08 |
NimbleGen, Inc. |
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
 |
Oligo Array |
in situ oligonucleotide, NIMBLE_MMCCSAL01_380k, This set includes 386350 46~50mer oligonucleotides, mostly 50-mers. The probes were designed based on Salmonella typhimurium LT2 (NC_003197.1) genome, with a moving window of about 12 bases. ONLY the SalmP probes are represented in this file. |
| 16 |
GPL5647 |
Ecoli_pangenome_CBSDTU_v1 |
385,979 |
DTU |
2007-07-24 |
NimbleGen |
Escherichia coli
 |
Oligo Array |
in situ oligonucleotide, Ecoli_pangenome_CBSDTU_v1, |
| 17 |
GPL9409 |
Rhizobium etli CFN 42 385K 071203_ReCFN42JM_Tiling |
385,673 |
KULeuven |
2009-10-08 |
Nimblegen |
Rhizobium etli CFN 42
 |
Tiling Array |
in situ oligonucleotide, Rhizobium etli CFN 42 385K 071203_ReCFN42JM_Tiling, Whole genome expression tiling array for Rhizobium etli CFN42, representing the forward strand of the chromosome and all 6 plasmids (NC_007761, NC007762, NC_007763, NC_007764, NC_004041, NC_007765, NC_007766), included repeat regions, 60mers, Ctrl (RNA) probes replicated 50 times, ERCC probes replicated 6 times, probe interval 13bp |
| 18 |
GPL8468 |
NimbleGen Halobacterium 385K tiling array |
385,440 |
Institute for Systems Biology |
2009-04-22 |
Nimblegen |
Halobacterium sp. NRC-1
|
Tiling Array |
in situ oligonucleotide, NimbleGen Halobacterium 385K tiling array, 50mer oligo probe every 13nt. Native NimbleGen files (ndf, pos) are linked below as supplementary files. |
| 19 |
GPL8942 |
CBCB Listeria monocytogenes 385K v1.0 |
385,000 |
University of Maryland |
2009-07-28 |
Nimblegen |
Listeria monocytogenes,Listeria monocytogenes EGD-e,Listeria monocytogenes serotype 4b str. F2365,Listeria monocytogenes serotype 1/2a str. F6854,Listeria monocytogenes serotype 4b str. H7858,Listeria monocytogenes FSL F2-515,Listeria monocytogenes FSL J1
 |
Tiling Array |
in situ oligonucleotide, CBCB Listeria monocytogenes 385K v1.0, This array is a Listeria monocytogenes pan-genome tiling array covering the full genomes of 20 L. monocytogenes strains. Each probe on the array may target multiple strains. Each probe may contain either zero or one mismatch to its intended genomic targets. The whole genomes of all 20 strains are tiled at an average depth of coverage of 2.65x, and the 50-mer probes are offset on average 21 bp from one another. The tiled strains by GenBank TaxID are: 265669, 267409, 267410, 393116, 393117, 393118, 393119, 393120, 393122, 393123, 393124, 393125, 393128, 393130, 393131, 393132, 393133, 401650, 393121, 169963. IMPORTANT: The genomic positions in the data table only represent the position on a single genome. The supplementary files contain the mapping of probes to pan-genomic positions. The columns in the supplementary "probe_mapping" file are: ID_REF: Probe ID. Each probe can appear in multiple rows depending on how many genomes it targets. GI_RANGE: Sequence GenBank GI and probe mapping location. RANGE_STRAND: Strand on the GI sequence the probe maps to. MISMATCH: Number of mismatches between probe and genomic sequence, 0 or 1. |
| 20 |
GPL6392 |
CDC C. botulinum ATCC 3502 CGH 385k array version 1 |
384,771 |
Centers for Disease Control and Prevention |
2008-01-18 |
NimbleGen |
Clostridium botulinum A str. ATCC 3502
 |
Oligo Array |
in situ oligonucleotide, CDC C. botulinum ATCC 3502 CGH 385k array version 1, |