NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Platform GPL7117 Query DataSets for GPL7117
Status Public on Aug 05, 2008
Title JCVI Aspergillus flavus NRRL3357 27.6k oligo array
Technology type spotted oligonucleotide
Distribution non-commercial
Organisms Aspergillus flavus NRRL3357; Aspergillus oryzae RIB40
Manufacturer The J. Craig Venter Institute
Manufacture protocol The 70-mer oligo microarray was designed based on CDS annotated from the A. flavus NRRL 3357 whole genome sequence. A total of 12,160 oligos were synthesized by Invitrogen. They represent 12,125 sequences, including 11,837 A. flavus genes, 278 A. oryzae–specific genes (not present in A. flavus), and 10 corn genes that show resistance to A. flavus. The oligos were printed in duplicate on Corning glassUltraGAPs amino-silane coated slides at JCVI using a high density automated arrayer (Intelligent Automation, Cambridge, MA 02139).
Support glass
Coating aminosilane
 
Description At least one oligo was designed from each gene model larger then 100 amino acids. For genes with more than one exon, oligos were designed based on the second exon sequence. For genes bigger than 4 kb, two oligos were designed from 5’ and 3’ ends.
 
Contributor(s) Wan C, Sun C, Yu J, Niermann W, Fedorova N, Varga J
Submission date Aug 01, 2008
Last update date Aug 05, 2008
Contact name Natalie Fedorova
E-mail(s) [email protected]
Phone 301-795-7756
Fax 301-838-0208
Organization name JCVI
Department Infectious Disease
Street address 9704 Medical Center Dr
City Rockville
State/province MD
ZIP/Postal code 20850
Country USA
 

Data table header descriptions
ID
ROW Slide row
COLUMN Slide column
META ROW Block row
META COLUMN Block column
SUB ROW Sub row
SUB COLUMN Sub column
ORGANISM Organism used as a source of the oligonucleotide sequences
ORF GenBank locus-tag
SPOT ID Alternative IDs used in TIGR/JCVI databases
NAME Functional description of the gene
SEQUENCE Olignucleotide sequence
GB_ACC GenBank accession number
SPOT_ID

Data table
ID ROW COLUMN META ROW META COLUMN SUB ROW SUB COLUMN ORGANISM ORF SPOT ID NAME SEQUENCE GB_ACC SPOT_ID
20998 219 70 10 3 3 22 Zea mays Mo17 Corn_gene_005 Hypothetical protein GAAGGTGCCGTACGACTTCATCGTGTCGCTGATGAAGGATCTCGGAGGGGACTGGGACATCGACTACATG AY104771.1
21755 227 59 10 3 11 11 Zea mays Mo17 Corn_gene_005 Hypothetical protein GAAGGTGCCGTACGACTTCATCGTGTCGCTGATGAAGGATCTCGGAGGGGACTGGGACATCGACTACATG AY104771.1
2950 31 70 2 3 7 22 Zea mays Mo17 Corn_gene_007 Aldose reductase GGAAGAACGACAGGATCTTTGAGGCCTGCAAGAAGCATGGGATCCATGTTACTGCTTACTCTCCGCTGGG AY109728.1
3707 39 59 2 3 15 11 Zea mays Mo17 Corn_gene_007 Aldose reductase GGAAGAACGACAGGATCTTTGAGGCCTGCAAGAAGCATGGGATCCATGTTACTGCTTACTCTCCGCTGGG AY109728.1
16774 175 70 8 3 7 22 Zea mays Mo17 Corn_gene_010 Heat shock protein CTAGCAACGAAGCAGAAATGTCGCTGGTGAGGCGCAGCAGCGTGTTCGACCCATTCTCCGTGGACCTCT AY111665.1
17531 183 59 8 3 15 11 Zea mays Mo17 Corn_gene_010 Heat shock protein CTAGCAACGAAGCAGAAATGTCGCTGGTGAGGCGCAGCAGCGTGTTCGACCCATTCTCCGTGGACCTCT AY111665.1
11782 123 70 6 3 3 22 Zea mays Mo17 Corn_gene_003 Glyoxalase GlxI GCTCAGGTTGCCATTGGCACCAATGATGTGTACAAGAGCGCTGAGGCAGTTGATCTGGCGACCAAAGAAC AY241545.1
12539 131 59 6 3 11 11 Zea mays Mo17 Corn_gene_003 Glyoxalase GlxI GCTCAGGTTGCCATTGGCACCAATGATGTGTACAAGAGCGCTGAGGCAGTTGATCTGGCGACCAAAGAAC AY241545.1
2566 27 70 2 3 3 22 Zea mays Mo17 Corn_gene_001 Pathogenesis-related protein CCTGATCGATCAAACAGCTAAGCGCACGACGTCGTGCGGCTCTCGTTGCAGTCATGCCGTTCAGCTTCAT AY953127.1
3323 35 59 2 3 11 11 Zea mays Mo17 Corn_gene_001 Pathogenesis-related protein CCTGATCGATCAAACAGCTAAGCGCACGACGTCGTGCGGCTCTCGTTGCAGTCATGCCGTTCAGCTTCAT AY953127.1
7174 75 70 4 3 3 22 Zea mays Mo17 Corn_gene_002 Pathogenesis-related protein CCAAGAAGGGCTACCTCCGTTTCACCAAGGTTTAGCTAGCCGACGCACGGCACGGACATCTAGCTCGTCT BT016686.1
7931 83 59 4 3 11 11 Zea mays Mo17 Corn_gene_002 Pathogenesis-related protein CCAAGAAGGGCTACCTCCGTTTCACCAAGGTTTAGCTAGCCGACGCACGGCACGGACATCTAGCTCGTCT BT016686.1
12166 127 70 6 3 7 22 Zea mays Mo17 Corn_gene_009 Heat shock protein CTGAAGAAGGAGGAGGTCAAGGTGGAGGTCGAGGACGGCAACGTCCTTCAGATCAGCGGCGAGCGCAACA BT016867.1
12923 135 59 6 3 15 11 Zea mays Mo17 Corn_gene_009 Heat shock protein CTGAAGAAGGAGGAGGTCAAGGTGGAGGTCGAGGACGGCAACGTCCTTCAGATCAGCGGCGAGCGCAACA BT016867.1
7558 79 70 4 3 7 22 Zea mays Mo17 Corn_gene_008 Hypothetical protein CGCTGCATCACCATCGGTCGATCGATCAGCCTTTCCCATGCATGTCTCGTATACTACACGTCTACACGTG MZ56820
8315 87 59 4 3 15 11 Zea mays Mo17 Corn_gene_008 Hypothetical protein CGCTGCATCACCATCGGTCGATCGATCAGCCTTTCCCATGCATGTCTCGTATACTACACGTCTACACGTG MZ56820
25606 267 70 12 3 3 22 Zea mays Mo17 Corn_gene_006 Trypsin inhibitor, Hageman factor inhibitor CCTGGATTCTCGGCGGCGGAACGATGCCCTCCAAGTAACTGCGAAGAGCATAGTGCATGAGGAATGAGCT NM_001112762.1
26363 275 59 12 3 11 11 Zea mays Mo17 Corn_gene_006 Trypsin inhibitor, Hageman factor inhibitor CCTGGATTCTCGGCGGCGGAACGATGCCCTCCAAGTAACTGCGAAGAGCATAGTGCATGAGGAATGAGCT NM_001112762.1
1 1 1 1 1 1 1 Aspergillus flavus NRRL3357 AFLA_008960 1739.m00153 TPR domain protein CTACAACGGAAAGATCGTTGACGTACTTGGTGTGGCTTCTGCTATGCTAGAAGGAGAAATTGAATATCGG
2 1 2 1 1 1 2 Aspergillus flavus NRRL3357 AFLA_022330 1866.m00910 conserved hypothetical protein TCTGCGTTCGACTACGCATTCTTCTGTCAATCGTTCGGCGGGCAGTTTGTCAATGTTTACCGATATGGCG

Total number of rows: 27648

Table truncated, full table size 4457 Kbytes.




Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp

Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap