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Status
Public on Feb 08, 2006
Title
NADC MAP Oligo v1.0
Technology type
spotted oligonucleotide
Distribution
non-commercial
Organisms
Mycobacterium avium subsp. paratuberculosis ; Mycobacterium avium subsp. avium Manufacturer
National Animal Disease Center, USDA-ARS
Manufacture protocol
70mer oligos were designed using ArrayOligoSelector. Input sequences included all annotated ORFs and intergenic regions > 500 bp from MAP K10 as well as all MAA 104 ORFs with < 30% identity to MAP K10. MAA 104 sequence was obtained from TIGR on 07/09/04 and automatically annotated using Reganor software (McHardy et al). One oligo was designed for each ORF < 2000 bp and two oligos were designed for each ORF > 2000 bp. Six Arabidopsis clones and MAP K10 sheared genomic DNA are included as controls. Oligos were synthesized by Illumina. The microarray was printed using a BioRobotics arrayer equiped with 48 quill tip pins. Each source well was printed in triplicate on the array.
Support
glass
Coating
other
Contributor(s)
Paustian ML , Bannantine JP , Kapur V Submission date
Feb 07, 2006
Last update date
Apr 01, 2008
Contact name
Mike Paustian
E-mail(s)
mpaustia@nadc.ars.usda.gov Organization name
National Animal Disease Center, USDA-ARS
Street address
2300 Dayton Ave
City
Ames
State/province
IA
ZIP/Postal code
50010
Country
USA
Samples (161)
GSM172202 , GSM172203 , GSM172204 , GSM172205 , GSM172206 , GSM172207
GSM172208 ,
GSM172209 ,
GSM172210 ,
GSM172211 ,
GSM172212 ,
GSM172213 ,
GSM172214 ,
GSM172215 ,
GSM172216 ,
GSM172217 ,
GSM172218 ,
GSM172219 ,
GSM172220 ,
GSM172221 ,
GSM172222 ,
GSM172223 ,
GSM172224 ,
GSM172225 ,
GSM172226 ,
GSM172227 ,
GSM172228 ,
GSM172229 ,
GSM172230 ,
GSM172231 ,
GSM172232 ,
GSM172233 ,
GSM172234 ,
GSM172235 ,
GSM172236 ,
GSM172237 ,
GSM172238 ,
GSM172239 ,
GSM172240 ,
GSM172241 ,
GSM172242 ,
GSM172243 ,
GSM172244 ,
GSM172245 ,
GSM172246 ,
GSM172247 ,
GSM172248 ,
GSM172249 ,
GSM172250 ,
GSM172251 ,
GSM172252 ,
GSM172253 ,
GSM172254 ,
GSM172255 ,
GSM172256 ,
GSM172257 ,
GSM172258 ,
GSM172259 ,
GSM172260 ,
GSM172261 ,
GSM172262 ,
GSM172263 ,
GSM172264 ,
GSM172265 ,
GSM172266 ,
GSM172267 ,
GSM172268 ,
GSM172269 ,
GSM172270 ,
GSM172271 ,
GSM172272 ,
GSM172273 ,
GSM172274 ,
GSM172275 ,
GSM172276 ,
GSM172277 ,
GSM172278 ,
GSM172279 ,
GSM172280 ,
GSM172281 ,
GSM172282 ,
GSM172283 ,
GSM172284 ,
GSM172285 ,
GSM172286 ,
GSM172287 ,
GSM172288 ,
GSM172289 ,
GSM172290 ,
GSM172291 ,
GSM172292 ,
GSM172293 ,
GSM172294 ,
GSM172295 ,
GSM172296 ,
GSM172297 ,
GSM172298 ,
GSM172299 ,
GSM172300 ,
GSM172301 ,
GSM172302 ,
GSM172303 ,
GSM172304 ,
GSM172305 ,
GSM172306 ,
GSM172307 ,
GSM172308 ,
GSM172309 ,
GSM172310 ,
GSM172311 ,
GSM172312 ,
GSM172313 ,
GSM172314 ,
GSM172315 ,
GSM172316 ,
GSM172317 ,
GSM172318 ,
GSM172319 ,
GSM172320 ,
GSM172321 ,
GSM172322 ,
GSM172323 ,
GSM172324 ,
GSM172325 ,
GSM172326 ,
GSM172327 ,
GSM172328 ,
GSM172329 ,
GSM172330 ,
GSM172331 ,
GSM172332 ,
GSM172333 ,
GSM172334 ,
GSM172335 ,
GSM172336 ,
GSM172337 ,
GSM172338 ,
GSM172339 ,
GSM172340 ,
GSM172341 ,
GSM172342 ,
GSM172343 ,
GSM172344 ,
GSM1529412 ,
GSM1529413 ,
GSM1529414 ,
GSM1529415 ,
GSM1529416 ,
GSM1529417 ,
GSM1529418 ,
GSM1529419 ,
GSM1529420 ,
GSM1529421 ,
GSM1529422 ,
GSM1529423 ,
GSM1529424 ,
GSM1529425 ,
GSM1529426 ,
GSM1529427 ,
GSM1529428 ,
GSM1529429 Series (2)
GSE7622 Comparative genomic hybridizations of Mycobacterium avium isolates obtained from multiple host species
GSE62566 Characterization of the inflammatory phenotype of Mycobacterium avium subspecies paratuberculosis
Data table header descriptions ID sa Array Row sa Array Column sa Spot Row sa Spot Column gpr Block gpr Column gpr Row PlateID SPOT_ID Spot identification - usually the ORF number
GB_ACC Genbank accession number (if available)
GENOME_ACC Accession.version[ORF_START..ORF_END]
ORGANISM Organism that the sequence was annotated from
ORF ORF_START ORF start coordinates
ORF_END ORF end coordinates
COMMENT Additional information regarding the oligos
PT_GI_LIST Genbank GI designation (if available)
Data table ID sa Array Row sa Array Column sa Spot Row sa Spot Column gpr Block gpr Column gpr Row PlateID SPOT_ID GB_ACC GENOME_ACC ORGANISM ORF ORF_START ORF_END COMMENT PT_GI_LIST 1
1
1
1
1
1
1
1
13I24
MAP3721
AE016958.1
Mycobacterium avium subsp. paratuberculosis
MAP3721
4140311
4141786
41409819 2
1
1
1
2
1
2
1
13M24
MAP3816
AE016958.1
Mycobacterium avium subsp. paratuberculosis
MAP3816
4264949
4265191
41409914 3
1
1
1
3
1
3
1
14A12
MAP3893c_5p
AE016958.1
Mycobacterium avium subsp. paratuberculosis
MAP3893c
4356884
4359175
41409991 4
1
1
1
4
1
4
1
14E12
MAP3985c
AE016958.1
Mycobacterium avium subsp. paratuberculosis
MAP3985c
4443184
4444128
41410083 5
1
1
1
5
1
5
1
14I12
MAP4077c_3p
AE016958.1
Mycobacterium avium subsp. paratuberculosis
MAP4077c
4544877
4547252
41410175 6
1
1
1
6
1
6
1
14M12
MAP4168
AE016958.1
Mycobacterium avium subsp. paratuberculosis
MAP4168
4642379
4642795
41410266 7
1
1
1
7
1
7
1
14A24
MAP3904
AE016958.1
Mycobacterium avium subsp. paratuberculosis
MAP3904
4367269
4367601
41410002 8
1
1
1
8
1
8
1
14E24
MAP3997c
AE016958.1
Mycobacterium avium subsp. paratuberculosis
MAP3997c
4454110
4455021
41410095 9
1
1
1
9
1
9
1
14I24
MAP4089
AE016958.1
Mycobacterium avium subsp. paratuberculosis
MAP4089
4559674
4561212
41410187 10
1
1
1
10
1
10
1
14M24
MAP4179
AE016958.1
Mycobacterium avium subsp. paratuberculosis
MAP4179
4652705
4653268
41410277 11
1
1
1
11
1
11
1
15A12
MAP4261
AE016958.1
Mycobacterium avium subsp. paratuberculosis
MAP4261
4730626
4731252
41410359 12
1
1
1
12
1
12
1
15E12
AY056187
AY056187 Arabidopsis thaliana
Clones corresponding to the Arabidopsis controls can be ordered from the RIKEN or TAIR public repositories
13
1
1
1
13
1
13
1
emp
-- empty
14
1
1
1
14
1
14
1
emp
-- empty
15
1
1
1
15
1
15
1
15A24
MAP4273c
AE016958.1
Mycobacterium avium subsp. paratuberculosis
MAP4273c
4740921
4741229
41410371 16
1
1
1
16
1
16
1
15E24
MAP4350c
AE016958.1
Mycobacterium avium subsp. paratuberculosis
MAP4350c
4829033
4829176
41410448 17
1
1
1
17
1
17
1
emp
-- empty
18
1
1
1
18
1
18
1
emp
-- empty
19
1
1
1
19
1
19
1
emp
-- empty
20
1
1
2
1
1
1
2
11M12
MAP3065
AE016958.1
Mycobacterium avium subsp. paratuberculosis
MAP3065
3410686
3411987
41409163
17328 2688 Kbytes .Supplementary data files not provided
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