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Platform GPL6990 Query DataSets for GPL6990
Status Public on Jun 02, 2009
Title Clostridium beijerinckii NCIMB 8052 Spotted Oligonucleotide Array v1
Technology type spotted oligonucleotide
Distribution non-commercial
Organism Clostridium beijerinckii NCIMB 8052
Manufacturer University of Illinois Functional Genomics Center Microarray Facility
Manufacture protocol An oligonucleotide of 70 bp was designed as a probe specific for each gene. Each probe was made on the forward strand of the gene. A probe was selected based on global optimization from all combinations of 70-mer within the target sequence by scoring simultaneously for a set of criteria including melting temperature, presence of hairpin/secondary structure, presence of low-complexity sequence and sequence specificity with respect to other genes. Sequence specificity was examined by sequence alignment using BLAST to ensure that the selected probe is different from all other sequences in the set beyond a certain value. All 70-mer probes have very similar melting temperature of ~65 oC. The oligonucleotides were synthesized (Invitrogen) and printed as duplicates onto glass slides. The slides were hybridized using probes generated by an aminoallyl-labeling and Cy dye-coupling procedure adapted from a TIGR protocol. Hybridized slides were scanned on an Axon Microarray Scanner. Features were extracted using GenePix Pro.
Support glass
Coating unknown
 
Description The draft genome sequence assembly of Clostridium beijerinckii (whole genome shotgun [WGS] project accession AALO00000000) was used as a source of the genes used in this study. Note, this WGS project has been superceded by the complete genome in (non-WGS) GenBank record CP000721.
The Platform data table reflects a condensed representation of the array's replicate features. The full array layout representing all of the individual features is linked as a supplementary file at the foot of this record.
 
Contributor(s) Shi Z, Blaschek H
Submission date Jun 24, 2008
Last update date Jun 02, 2009
Contact name Zhen Shi
E-mail(s) zshi@illinois.edu
Organization name University of Illinois
Department Institute for Genomic Biology
Street address 1206 West Gregory Drive
City Urbana
State/province IL
ZIP/Postal code 61801
Country USA
 
Samples (21) GSM309614, GSM310379, GSM310380, GSM310381, GSM310382, GSM310383 
Series (3)
GSE12358 Clostridium beijerinckii NCIMB 8052 wild-type fermentation time course
GSE12359 Clostridium beijerinckii BA101 mutant fermentation time course
GSE12365 Clostridium beijerinckii fermentation time course

Data table header descriptions
ID
Annotation Annotation of gene
ORF_ID Identification number assigned to annotated gene
SEQUENCE oligo seqeunce

Data table
ID Annotation ORF_ID SEQUENCE
1 Acetyl-CoA carboxylase beta subunit 1246 TCTGAAGAAAAGCCTAATATACCATCAGGTATGTGGGAAAAATGTGATAAGTGTAATTCAATGATATATG
2 Co-chaperonin groES, hsp10 family 2270 ATGAACATTAAACCACTTGGTGAAAGAGTAGTAATTAAAAAATTAGAGGCAGAAGAAAAGACTAAGAGTG
3 ABC-type probable sulfate transporter, permease protein 3059 ACTTTATCAACAGCAGCATTCTTTGTAATTTGGTATTTAGCGACTTCAACTGGAATTTTAGATACTGGAA
4 Alpha-glucosidase 4142 AGTACTAAAATAGAAGATGATGTTGTAACTCTTTATGCACCATGTAATAAGATAAACCAACGAGGAGATA
5 3-Oxoacyl-[acyl-carrier-protein] synthase II 1242 TAACTTTAGTTGATAAAGATTTAGTAGATGTAAAAATAGCAGCAGAAGTTAAGGGCTTTGATCCAGATAC
6 Pyruvate formate-lyase 2257 GACACTCATTAGAGGATGTCATTAGACAGAGATATGGAAAAGAAATTGATGAAATTGCAAAAGTGGTAAA
7 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase 3044 TTTTGGGATTGCACCAAAATCAGAAGGAAATGCTGTAACTTTAGCGAAAAAGCCAAATTTAGATAAACTA
8 Nitroreductase family protein 4070 CTACATAGTAGTGAAATCTGAAGAAATGAGACAAAAAATAGTAGAGGCTTCTCATAATCAAAAATGGATG
9 3-Oxoacyl-[acyl-carrier-protein] synthase III 1238 TAGTTACTAATGATAGAATAAGTGAATTCGTTGAAACAAGTGATGAGTGGATAGTGCAAAGAACAGGTAT
10 3-Oxoacyl-(acyl carrier protein) reductase 2207 TTATTATGATGAAGAATATGTACCAAAGTATAGTGAGAGTGATTTATTGCAGCATCCATCAGGCAGAATA
11 VanW like protein family 3037 ATTTCCTTCAAAGAAGGGGATTTTATAATGTTTGGAAGAGAATCTAGTGGAGTTCCTGAAGAAGTGCATA
12 Zinc-binding dehydrogenase, alcohol dehydrogenase 4030 TTGAGTTAATACAAACGGAAATTCCAGAACCAACTAAAAATCAAGTAAGGATAAAAATTCTAGCTTGTGG
13 Predicted FeS oxidoreductase 111 AAAATAGAAATAGCGAAGAATAGAGAACAATATAATGAAGAGGCTTCAAGCAAGTATAAAGTTGGAATGG
14 Nitrogenase iron protein, nifH 2169 ACAAACAGTTATAGAATTTGATCCAAAAGCTGATCAAGCAGATGAATACAGAACATTGGCTAAGAATATA
15 Ribulose-phosphate 3-epimerase family protein 2995 TACATTGCGATGTAATGGATGGAGTTTTTGTTAACAATTTAGCTATGGGACCTTATGTATTGGAACAAAT
16 Acetoacetate decarboxylase 4002 TCATATACAGAATGTGGTCAAGCTATTCCAGTAAAATATAATGGTGTTAAGGGTGACTACTTGCATATGA
17 Cyclopropane fatty acid synthase 1079 TTATTAAATGATAAGGGTGTATCTTTACTTCACTGCATAACATCAACAGAGGTTGGAGGAAATAATACAT
18 FeMo cofactor synthesis protein, nifE 2164 CTCCCTAAGAGAAAAGGAATTAATATGTTAGGAGATTTCAATTTAGCTGGTGAAATATGGATTGTTAAAG
19 Transketolase N-terminal section 2989 GGATGGAATGTTGTAACTATAGATGGACATTGTTTTGAAGATATAAGTAAAGCCATAGATGATGCTAATG
20 ABC transporter, ATP-binding protein 3993 TACTTAATGAACGTACTGATTCTATACTAAAAAGGTTAGAGCTGCTAGAGGTAAAAGATAAGAAGGTGAA

Total number of rows: 484

Table truncated, full table size 55 Kbytes.




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

Supplementary file Size Download File type/resource
GPL6990_full_array_layout.txt.gz 12.9 Kb (ftp)(http) TXT

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