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Platform GPL2981 Query DataSets for GPL2981
Status Public on Apr 17, 2006
Title Dichelobacter nodosus oligonucleotide microarray
Technology type spotted oligonucleotide
Distribution non-commercial
Organism Dichelobacter nodosus
Manufacturer Micromon
Manufacture protocol Microarrays were constructed in house and consisted of 2,317 custom 70-mer oligonucleotides (designed to reduce cross-hybridisation; Gary Myers and Ian Paulsen, TIGR) spotted in triplicate with 50% DMSO on Ultra-GAPS slides (Corning) using a QArray Mini (Genetix) arrayer, representing 1,343 ORFs, as determined from the unpublished D. nodosus genome sequence (http://www.tigr.org).
Support glass
Coating aminosilane
 
Description Microarrays consisted of 2,317 custom 70-mer oligonucleotides (designed to reduce cross-hybridisation) spotted in triplicate on Ultra-GAPS slides (Corning) using a QArray Mini (Genetix) arrayer, representing 1,343 ORFs as determined from the unpublished D. nodosus genome sequence (http://www.tigr.org) and where possible two gene probes per ORF were synthesised. Oligonucleotides were spotted on a 2X6 metagrid, which was composed of 24X26 subgrids.
 
Contributor(s) Parker D, Kennan RM, Myers GS, Paulsen IT, Rood JI
Submission date Oct 17, 2005
Last update date Apr 17, 2006
Contact name Julian I Rood
E-mail(s) julian.rood@monash.edu
Phone 61 3 990 29157
Organization name Monash University
Department Microbiology
Lab Rood
Street address Wellington Road
City Melbourne
State/province Victoria
ZIP/Postal code 3800
Country Australia
 
Samples (25) GSM78497, GSM78498, GSM78499, GSM78500, GSM78501, GSM78502 
Series (3)
GSE3465 D. nodosus WT vs rpoN mutant
GSE3466 D. nodosus WT vs pilR mutant
GSE5157 JIR1201, JIR1212, JIR1244, JIR1461, JIR1474, JIR3209, JIR3350, JIR3356 and JIR3528 genomic arrays

Data table header descriptions
ID
Block Block number on array
Row Row position on array
Column Column position on array
ORF number ORF number or genomic DNA (JIR, VCS) with concentration
Gene Gene number
Name Automated annotation of ORF
Plate Plate number in which oligonucleotides are stored
Well Well in plate that oligonucleotide is located
SEQUENCE Sequence 5' to 3' of oligonucleotide
SPOT_ID

Data table
ID Block Row Column ORF number Gene Name Plate Well SEQUENCE SPOT_ID
1 1 1 1 JIR-50ng/ul JIR-50ng/ul -- CONTROL
2 1 1 2 JIR-50ng/ul JIR-50ng/ul -- CONTROL
3 1 1 3 JIR-50ng/ul JIR-50ng/ul -- CONTROL
4 1 1 4 JIR-25ng/ul JIR-25ng/ul -- CONTROL
5 1 1 5 JIR-25ng/ul JIR-25ng/ul -- CONTROL
6 1 1 6 JIR-25ng/ul JIR-25ng/ul -- CONTROL
7 1 1 7 JIR-12.5ng/ul JIR-12.5ng/ul -- CONTROL
8 1 1 8 JIR-12.5ng/ul JIR-12.5ng/ul -- CONTROL
9 1 1 9 JIR-12.5ng/ul JIR-12.5ng/ul -- CONTROL
10 1 1 10 JIR-6.25ng/ul JIR-6.25ng/ul -- CONTROL
11 1 1 11 JIR-6.25ng/ul JIR-6.25ng/ul -- CONTROL
12 1 1 12 JIR-6.25ng/ul JIR-6.25ng/ul -- CONTROL
13 1 1 13 VCS-50ng/ul VCS-50ng/ul -- CONTROL
14 1 1 14 VCS-50ng/ul VCS-50ng/ul -- CONTROL
15 1 1 15 VCS-50ng/ul VCS-50ng/ul -- CONTROL
16 1 1 16 VCS-25ng/ul VCS-25ng/ul -- CONTROL
17 1 1 17 VCS-25ng/ul VCS-25ng/ul -- CONTROL
18 1 1 18 VCS-25ng/ul VCS-25ng/ul -- CONTROL
19 1 1 19 VCS-12.5ng/ul VCS-12.5ng/ul -- CONTROL
20 1 1 20 VCS-12.5ng/ul VCS-12.5ng/ul -- CONTROL

Total number of rows: 7488

Table truncated, full table size 985 Kbytes.




Download family Format
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Supplementary data files not provided
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