Based on the genome sequence of A. niger CBS513.88, a proprietary GeneChip®, dsmM_ANIGERa_coll511030F, was designed for DSM according to the GeneChip® CustomExpress™ program by Affymetrix (Affymetrix, Inc., Santa Clara, CA). The chips of the 49 format contain 11μm features. There are 12 pairs of 25-oligonucleotides in each probe set representing each of approximately 14259 annotated ORFs and genetic elements of A. niger. The probe sequences were designed based on maximally the 600 bp region in the (predicted) coding sequence stretching from the 3’-end. Typical Affymetrix control probe sets were included (B. subtilis, E. coli, Bacteriophage P1 and A. thaliana spike controls). For several constitutive A. niger genes, separate 3’-end, middle and 5’-end probe sets were designed that allow monitoring of the efficiency of the in vitro transcription reaction. Genes of one gene family can be represented by a unique and a shared probe set. In total 14554 probesets are measured through the dsmM_ANIGERa_coll511030F GeneChip®.
The transcriptional repressor TupA in Aspergillus niger is involved in controlling gene expression related to cell wall biosynthesis, development, and nitrogen source availability
Comparative study of gene expression in Aspergillus niger solid and submerged growth during sugar beet pulp utilization
Data table header descriptions
ID
DESCRIPTION
description of represented gene
Gene_ACC
Aspergillus niger CBS513.88 gene/protein identifier, recognized in GeneBank datatabase
GI
Genbank identifier
ORGANISM
Source organism
SEQUENCE_TYPE
type of element recognoized by the probe set
ORF
SPOT_ID
PROBESETCOUNT
number of probe sets recognizing this gene
PROBESETSCORE
Affymetrix probe set quality score
Data table
ID
DESCRIPTION
Gene_ACC
GI
ORGANISM
SEQUENCE_TYPE
ORF
SPOT_ID
PROBESETCOUNT
PROBESETSCORE
AFFX-BioB-5_at
J04423 E coli bioB gene biotin synthetase (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-BioB-5_at
Affy hyb control
Affy hyb control
2
AFFX-BioB-M_at
J04423 E coli bioB gene biotin synthetase (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-BioB-M_at
Affy hyb control
Affy hyb control
2
AFFX-BioB-3_at
J04423 E coli bioB gene biotin synthetase (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-BioB-3_at
Affy hyb control
Affy hyb control
2
AFFX-BioC-5_at
J04423 E coli bioC protein (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-BioC-5_at
Affy hyb control
Affy hyb control
2
AFFX-BioC-3_at
J04423 E coli bioC protein (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-BioC-3_at
Affy hyb control
Affy hyb control
2
AFFX-BioDn-5_at
J04423 E coli bioD gene dethiobiotin synthetase (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-BioDn-5_at
Affy hyb control
Affy hyb control
2
AFFX-BioDn-3_at
J04423 E coli bioD gene dethiobiotin synthetase (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-BioDn-3_at
Affy hyb control
Affy hyb control
2
AFFX-CreX-5_at
X03453 Bacteriophage P1 cre recombinase protein (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-CreX-5_at
Affy hyb control
Affy hyb control
2
AFFX-CreX-3_at
X03453 Bacteriophage P1 cre recombinase protein (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-CreX-3_at
Affy hyb control
Affy hyb control
2
AFFX-DapX-5_at
L38424 B subtilis dapB, jojF, jojG genes corresponding to nucleotides 1358-3197 of L38424 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-DapX-5_at
Affy spike control
Affy spike control
2
AFFX-DapX-M_at
L38424 B subtilis dapB, jojF, jojG genes corresponding to nucleotides 1358-3197 of L38424 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-DapX-M_at
Affy spike control
Affy spike control
2
AFFX-DapX-3_at
L38424 B subtilis dapB, jojF, jojG genes corresponding to nucleotides 1358-3197 of L38424 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-DapX-3_at
Affy spike control
Affy spike control
2
AFFX-LysX-5_at
X17013 B subtilis lys gene for diaminopimelate decarboxylase corresponding to nucleotides 350-1345 of X17013 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-LysX-5_at
Affy spike control
Affy spike control
2
AFFX-LysX-M_at
X17013 B subtilis lys gene for diaminopimelate decarboxylase corresponding to nucleotides 350-1345 of X17013 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-LysX-M_at
Affy spike control
Affy spike control
2
AFFX-LysX-3_at
X17013 B subtilis lys gene for diaminopimelate decarboxylase corresponding to nucleotides 350-1345 of X17013 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-LysX-3_at
Affy spike control
Affy spike control
2
AFFX-PheX-5_at
M24537B subtilis pheB, pheA genes corresponding to nucleotides 2017-3334 of M24537 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-PheX-5_at
Affy spike control
Affy spike control
2
AFFX-PheX-M_at
M24537B subtilis pheB, pheA genes corresponding to nucleotides 2017-3334 of M24537 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-PheX-M_at
Affy spike control
Affy spike control
2
AFFX-PheX-3_at
M24537B subtilis pheB, pheA genes corresponding to nucleotides 2017-3334 of M24537 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-PheX-3_at
Affy spike control
Affy spike control
2
AFFX-ThrX-5_at
X04603 B subtilis thrC, thrB genes corresponding to nucleotides 248-2229 of X04603 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-ThrX-5_at
Affy spike control
Affy spike control
2
AFFX-ThrX-M_at
X04603 B subtilis thrC, thrB genes corresponding to nucleotides 248-2229 of X04603 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
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