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Status
Public on Feb 10, 2008
Title
[AsprgDTUa520520F] Custom Affymetrix Aspergillus Chip DTU_3Aspergillus_45K_v1.0
Technology type
in situ oligonucleotide
Distribution
custom-commercial
Organisms
Aspergillus niger ; Aspergillus oryzae ; Aspergillus nidulans Manufacturer
Affymetrix
Manufacture protocol
Initial probe-design was done using the OligoWiz 2.0 software (Nielsen, 2003, Wernersson, 2005) from CDS sequences of predicted ORFs from the genome sequences of A. nidulans FGSC A4 (Galagan, 2005), A. niger ATCC 1015 (Baker, 2006) and A. oryzae RIB40 (Machida, 2005). For each gene, a maximum of 11 non-overlapping perfect match probes were calculated using the OligoWiz standard scoring of cross-hybridization, melting temperature, folding, position preference and low complexity. A 3' position preference for the probes was included in the computations. The probes were designed separately for each genome. Pruning of the probe sequences to comply with Affymetrix recommendations was done by removing duplicate probe sequences and shortening probes that were not possible to synthesize in full length. Also included on the chip iss a number of Affymetrix standard controls, custom controls, an A. oryzae EST-collection (courtesy of Novozymes A/S) and probes for ORFs from the S. coelicolor A3(2) (Bentley, 2002) genome.
Catalog number
AspergDTUa520520F
Support
glass
Coating
quartz
Description
Type: CustomExpress. Feature size: 11-micron. Format: 49-7875
Contributor(s)
Andersen MR , Wongsangnak W , Panagiotou G , Borodina I , Nielsen J Submission date
Oct 09, 2007
Last update date
Mar 23, 2010
Contact name
Mikael R Andersen
E-mail(s)
mr@bio.dtu.dk Organization name
Technical University of Denmark
Department
BioCentrum-DTU
Lab
Center for Microbial Biotechnology
Street address
Søltofts plads, bygn 223
City
Kgs. Lyngby
ZIP/Postal code
2800
Country
Denmark
Samples (176)
GSM235475 , GSM235476 , GSM235477 , GSM235478 , GSM235479 , GSM235481
GSM235482 ,
GSM235484 ,
GSM235485 ,
GSM235487 ,
GSM235489 ,
GSM235491 ,
GSM235494 ,
GSM235496 ,
GSM235497 ,
GSM235498 ,
GSM235499 ,
GSM235500 ,
GSM278104 ,
GSM278105 ,
GSM278106 ,
GSM278107 ,
GSM278108 ,
GSM278109 ,
GSM297399 ,
GSM297400 ,
GSM297401 ,
GSM297402 ,
GSM297403 ,
GSM297404 ,
GSM297563 ,
GSM297564 ,
GSM297565 ,
GSM301455 ,
GSM301456 ,
GSM301457 ,
GSM301458 ,
GSM301459 ,
GSM301460 ,
GSM301461 ,
GSM301462 ,
GSM301463 ,
GSM301464 ,
GSM301465 ,
GSM301466 ,
GSM301467 ,
GSM301468 ,
GSM301469 ,
GSM301470 ,
GSM301471 ,
GSM322544 ,
GSM322558 ,
GSM322559 ,
GSM322561 ,
GSM322562 ,
GSM322563 ,
GSM322564 ,
GSM322565 ,
GSM322568 ,
GSM322570 ,
GSM322572 ,
GSM322575 ,
GSM322576 ,
GSM322578 ,
GSM322591 ,
GSM322592 ,
GSM322593 ,
GSM322594 ,
GSM322596 ,
GSM322598 ,
GSM322601 ,
GSM322602 ,
GSM322603 ,
GSM348998 ,
GSM348999 ,
GSM349000 ,
GSM349001 ,
GSM349002 ,
GSM349003 ,
GSM349004 ,
GSM349005 ,
GSM349006 ,
GSM349007 ,
GSM349008 ,
GSM349009 ,
GSM349010 ,
GSM349011 ,
GSM349012 ,
GSM349013 ,
GSM349014 ,
GSM349015 ,
GSM393134 ,
GSM393135 ,
GSM393136 ,
GSM393137 ,
GSM393138 ,
GSM393139 ,
GSM393140 ,
GSM393141 ,
GSM393142 ,
GSM393143 ,
GSM393144 ,
GSM393145 ,
GSM393146 ,
GSM393147 ,
GSM393148 ,
GSM393149 ,
GSM393150 ,
GSM393151 ,
GSM498611 ,
GSM498612 ,
GSM498613 ,
GSM498614 ,
GSM498615 ,
GSM498616 ,
GSM498617 ,
GSM498618 ,
GSM498619 ,
GSM498620 ,
GSM498621 ,
GSM498622 ,
GSM498623 ,
GSM498624 ,
GSM498625 ,
GSM498626 ,
GSM498627 ,
GSM498628 ,
GSM498629 ,
GSM498630 ,
GSM498631 ,
GSM498632 ,
GSM498633 ,
GSM498634 ,
GSM498635 ,
GSM498636 ,
GSM498637 ,
GSM498638 ,
GSM498639 ,
GSM498640 ,
GSM498641 ,
GSM498642 ,
GSM498643 ,
GSM498644 ,
GSM498645 ,
GSM498646 ,
GSM525077 ,
GSM525078 ,
GSM525079 ,
GSM525080 ,
GSM525081 ,
GSM525082 ,
GSM525083 ,
GSM525084 ,
GSM525085 ,
GSM525086 ,
GSM560125 ,
GSM560126 ,
GSM560127 ,
GSM560128 ,
GSM560129 ,
GSM560130 ,
GSM560131 ,
GSM560132 ,
GSM560133 ,
GSM560134 ,
GSM560135 ,
GSM560136 ,
GSM1517944 ,
GSM1517945 ,
GSM1517946 ,
GSM1517947 ,
GSM1517948 ,
GSM1517949 ,
GSM1517950 ,
GSM1517951 ,
GSM1517952 Series (14)
GSE9275 A tri-species Aspergillus array (nidulans arrays)
GSE9276 A tri-species Aspergillus array (niger arrays)
GSE9277 A tri-species Aspergillus array (oryzae arrays)
GSE9298 A tri-species Aspergillus array
GSE10983 Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88
GSE11725 Study of the response of Aspergillus niger to three levels of ambient pH
GSE11930 Network-based analysis of carbohydrate-active gene transcription in Aspergillus niger
GSE12859 Studies on the production of fungal polyketides in Aspergillus nidulans using systems biology tools
GSE13868 Genome-wide analysis of maltose utilization and regulation in aspergilla
GSE15702 Expression data from batch cultivations with A. niger, A. oryzae and A. nidulans grown on glucose and glycerol
GSE19952 Expression data from batch cultivations of Aspergillus niger wild type and adrA, facB and creA deletion mutants
GSE21015 Expression data from batch cultivations with the acidogenic Aspergillus niger wild type strain ATCC 1015 and the areB complete deletion strain constructed using ATCC 1015 as background strain with glucose or glycerol as carbon sources.
GSE22566 Protein production by Aspergillus oryzae
GSE61985 Correlating citric acid formation and manganese limitation in Aspergillus niger using transcriptome and proteome analysis
Data table header descriptions ID DESCRIPTION The type of sequence used for feature probe design
ORGANISM The organism source of the feature
Internal_ORF ORF/locus name of the feature, if available. Can be used for accession from the respective genome web pages
ORF GenBank accession
SPOT_ID spot identifier
Data table ID DESCRIPTION ORGANISM Internal_ORF ORF SPOT_ID 23.ORF1_at
CDS
Streptomyces coelicolor
Streptomyces coelicolor ORF
23.ORF2_at
CDS
Streptomyces coelicolor
Streptomyces coelicolor ORF
23.ORF3_at
CDS
Streptomyces coelicolor
Streptomyces coelicolor ORF
23.ORF4_at
CDS
Streptomyces coelicolor
Streptomyces coelicolor ORF
AB164642_11059_at
CDS
Streptomyces coelicolor
AB164642
AB164642_12228_at
CDS
Streptomyces coelicolor
AB164642
AB164642_13346_at
CDS
Streptomyces coelicolor
AB164642
AB164642_13498_at
CDS
Streptomyces coelicolor
AB164642
AB164642_14751_at
CDS
Streptomyces coelicolor
AB164642
AB164642_15497_at
CDS
Streptomyces coelicolor
AB164642
AB164642_16915_at
CDS
Streptomyces coelicolor
AB164642
AB164642_1767_at
CDS
Streptomyces coelicolor
AB164642
AB164642_17798_at
CDS
Streptomyces coelicolor
AB164642
AB164642_19898_at
CDS
Streptomyces coelicolor
AB164642
AB164642_21201_at
CDS
Streptomyces coelicolor
AB164642
AB164642_22243_at
CDS
Streptomyces coelicolor
AB164642
AB164642_22665_at
CDS
Streptomyces coelicolor
AB164642
AB164642_23589_at
CDS
Streptomyces coelicolor
AB164642
AB164642_2380_at
CDS
Streptomyces coelicolor
AB164642
AB164642_3322_at
CDS
Streptomyces coelicolor
AB164642
43776 2742 Kbytes .Supplementary file Size Download File type/resource GPL5975_AspergDTUa520520F.cdf.gz
7.0 Mb
(ftp) (http) CDF
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