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Status
Public on Apr 01, 2009
Title
PNL mixed species lignin-degrading enzymes microarray
Technology type
spotted oligonucleotide
Distribution
non-commercial
Organisms
Cryphonectria parasitica ; Neurospora crassa ; Phlebia radiata ; Pleurotus ostreatus ; Pleurotus eryngii ; Trametes versicolor ; Schizophyllum commune ; Agaricus bisporus ; Lentinula edodes ; Fusarium oxysporum ; Trametes cinnabarina ; Heterobasidion annosum ; synthetic construct ; Botrytis cinerea ; Gelatoporia subvermispora ; Coriolopsis gallica ; Dichomitus squalens ; Trametes coccinea ; Fusarium proliferatum ; Phanerodontia chrysosporium Manufacturer
in-house, Pacific Northwest National Laboratory
Manufacture protocol
Probes were printed at 100 µM (in 100 mM Na2HPO4, 200 mM NaCl, 0.01% SDS print buffer) concentrations on epoxysilane-coated glass slides by a Microgrid II printing system (PerkinElmer Life And Analytical Sciences, Inc., Waltham, MA). Control spots were present as buffer, beacon, biotin, polyA and polyT oligonucleotides. The buffer spots were spots of blank print buffer (defined below) intended to ensure probe spots were well-spaced. The beacon spot was a spot of Cy3 dye (always fluorescent), used to identify the orientation of the slide. The biotin spot was included to check that biotin reporting was not hindered by the conditions used during hybridization or washing. PolyA and polyT probes were included as positive and negative controls for the polyA-modified eukaryotic genes that are then reverse-transcribed to generate polyT tagged cDNA.
Submission date
Dec 15, 2008
Last update date
Apr 01, 2009
Contact name
Katrina M Waters
E-mail(s)
katrina.waters@pnl.gov Organization name
Pacific Northwest National Laboratory
Department
Biological Sciences Division
Street address
902 Battelle Blvd; MSIN J4-18
City
Richland
State/province
WA
ZIP/Postal code
99352
Country
USA
Samples (68)
GSM351209 , GSM351210 , GSM351211 , GSM351212 , GSM351213 , GSM351214
GSM351215 ,
GSM351216 ,
GSM351217 ,
GSM351218 ,
GSM351219 ,
GSM351220 ,
GSM351221 ,
GSM351222 ,
GSM351223 ,
GSM351224 ,
GSM351225 ,
GSM351226 ,
GSM351227 ,
GSM351228 ,
GSM351229 ,
GSM351230 ,
GSM351231 ,
GSM351232 ,
GSM351233 ,
GSM351234 ,
GSM351235 ,
GSM351236 ,
GSM351237 ,
GSM351238 ,
GSM351239 ,
GSM351240 ,
GSM351241 ,
GSM351242 ,
GSM351243 ,
GSM351244 ,
GSM351245 ,
GSM351246 ,
GSM351247 ,
GSM351248 ,
GSM351249 ,
GSM351250 ,
GSM351251 ,
GSM351252 ,
GSM351253 ,
GSM351254 ,
GSM351255 ,
GSM351256 ,
GSM351257 ,
GSM351258 ,
GSM351259 ,
GSM351260 ,
GSM351261 ,
GSM351262 ,
GSM351263 ,
GSM351264 ,
GSM351265 ,
GSM351266 ,
GSM351267 ,
GSM351268 ,
GSM351269 ,
GSM351270 ,
GSM351271 ,
GSM351272 ,
GSM351273 ,
GSM351274 ,
GSM351275 ,
GSM351276 Series (1)
GSE13977 Expression of lignin-degrading enzymes in soils using targeted microarrays
Data table header descriptions ID PROBE probe name
SEQUENCE probe sequence
ORGANISM primary Genbank organism, source of probe sequence
GB_ACC GenBank Accession number
SPOT_ID
Data table ID PROBE SEQUENCE ORGANISM GB_ACC SPOT_ID 185
lac01
TTGCATCCGGTCATTCCT
Pycnoporus coccineus
AB072704 186
lac01
TTGCATCCGGTCATTCCT
Pycnoporus coccineus
AB072704 385
lac01
TTGCATCCGGTCATTCCT
Pycnoporus coccineus
AB072704 386
lac01
TTGCATCCGGTCATTCCT
Pycnoporus coccineus
AB072704 165
lac02
TCGCTTCGGGCCACTCGT
Pycnoporus cinnabarinus
AF152170 166
lac02
TCGCTTCGGGCCACTCGT
Pycnoporus cinnabarinus
AF152170 365
lac02
TCGCTTCGGGCCACTCGT
Pycnoporus cinnabarinus
AF152170 366
lac02
TCGCTTCGGGCCACTCGT
Pycnoporus cinnabarinus
AF152170 145
lac03
CCTATCCATCTCCACGGTCACG
Botryotinia fuckeliana
AF243855 146
lac03
CCTATCCATCTCCACGGTCACG
Botryotinia fuckeliana
AF243855 345
lac03
CCTATCCATCTCCACGGTCACG
Botryotinia fuckeliana
AF243855 346
lac03
CCTATCCATCTCCACGGTCACG
Botryotinia fuckeliana
AF243855 125
lac04
CACTGCCACATCGACTTCCAC
Conserved region in laccases, broad specificity
AY049725 126
lac04
CACTGCCACATCGACTTCCAC
Conserved region in laccases, broad specificity
AY049725 325
lac04
CACTGCCACATCGACTTCCAC
Conserved region in laccases, broad specificity
AY049725 326
lac04
CACTGCCACATCGACTTCCAC
Conserved region in laccases, broad specificity
AY049725 105
lac05
CTATTGCTTCCGGGCATTCA
Trametes versicolor
AY049725 106
lac05
CTATTGCTTCCGGGCATTCA
Trametes versicolor
AY049725 305
lac05
CTATTGCTTCCGGGCATTCA
Trametes versicolor
AY049725 306
lac05
CTATTGCTTCCGGGCATTCA
Trametes versicolor
AY049725
188 11 Kbytes .Supplementary data files not provided
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