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Platform GPL794 Query DataSets for GPL794
Status Public on Dec 22, 2004
Title CAGE-Xylella USP - v.2
Technology type spotted DNA/cDNA
Distribution non-commercial
Organism Xylella fastidiosa
 
Description DNA Microarray Construction. PCR primers were designed to amplify unique internal fragments of 200-1000 bp of each predicted CDS described in the annotated genome sequence of X. fastidiosa strain 9a5c (http://aeg.lbi.ic.unicamp.br/xf). Primers (18-23mers) with equivalent predicted melting temperature were designed with the use of a perl program that ran PRIMER3 (http://www-genome.wi.mit.edu/genome_software/other/primer3.html) for the complete CDS list, automatically testing many parameter settings and also guaranteeing that primers hybridized only to a single genome location. Oligonucleotides were synthesized by MWG and Operon Technologies. Genomic or cosmid DNA, obtained in the X. fastidiosa genome sequencing project (Simpson et al. 2000), were used as template in the first round of PCR amplification, and 200-fold-diluted PCR products were used as templates for PCR reamplification to increase product concentration when necessary. The reactions were done in 96-well plates. The mixture in each well contained 100 ng of DNA, 0.5 U of Biolase Taq polymerase (Bioline), 0.2 mM of each dNTP (Invitrogen), 1.5 mM MgCl2 and the primers at 0.5 uM, in a total volume of 100 ul. A 5min denaturing step at 95oC was applied, followed by 40 cycles of 95oC for 45s, 50oC for 30s, 72oC for 1min and a final step at 72oC for 10min. 4 ul of each PCR reaction were checked for product size and concentration by electrophoresis in 1.2% agarose gels. The amplicons were then purified with 96-well MultiScreen purification plates (Millipore) and an equal volume of dimethyl sulfoxide was added to the purified products (~100 ng/ul final concentration). Generation III DNA spotter (Amersham Biosciences) was used to array the samples onto coated type-7 glass slides (Amersham Biosciences). After deposition, the probes were crosslinked to the slides by applying 50 mJ of UV light and the slides were stored desiccated at ~10% relative humidity at room temperature until use.
Keywords = xylella fastidiosa
Keywords = genomotyping
Keywords = DNA microarray
Keywords = comparative genomics
 
Web link http://verjo19.iq.usp.br/cagexylella/
Contributor(s) Koide T, Zaini PA
Submission date Dec 22, 2003
Last update date Dec 12, 2007
Contact name Tie Koide
E-mail(s) tiekoide@gmail.com
Organization name Institute for Systems Biology
Street address 1441 N 34th street
City Seattle
State/province WA
ZIP/Postal code 98103
Country USA
 

Data table header descriptions
ID
MetaColumn sub-array column (total is 2)
MetaRow sub-array row (total is 12)
Column column (total is 32)
Row row (total is 12)
ORF Open reading frame
Gene Product Reporter Comments: gene product
Reporter Name name
PT_ACC Protein accession
PT_GI Protein identifier
SPOT_ID Control spots

Data table
ID MetaColumn MetaRow Column Row ORF Gene Product Reporter Name PT_ACC PT_GI SPOT_ID
1 1 1 1 1 XF2466 polygalacturonase precursor PGLA P20041
2 1 1 2 1 XF1328 cytochrome B561 YODB Q9PDQ1
3 1 1 3 1 XF1761 hypothetical protein XF1761 Q9PCL7
4 1 1 4 1 XF1330 hypothetical protein XF1330 Q9PDP9
5 1 1 5 1 XF1760 hypothetical protein XF1760 Q9PCL8
6 1 1 6 1 XF1332 uroporphyrinogen decarboxylase HEME Q9PDP7
7 1 1 7 1 XF1758 hypothetical protein XF1758 Q9PCM0
8 1 1 8 1 XF1344 ABC transporter sulfate binding protein sbp Q9PDN5
9 1 1 9 1 XF1757 hypothetical protein XF1757 Q9PCM1
10 1 1 10 1 XF1345 ABC transporter sulfate permease CYSU OR CYST Q9PDN4
11 1 1 11 1 XF1753 hypothetical protein XF1753 Q9PCM5
12 1 1 12 1 XF1346 ABC transporter sulfate permease CYSW OR SLR1454 Q9PDN3
13 1 1 13 1 XF1746 alcohol dehydrogenase YAHK Q9PCN2
14 1 1 14 1 XF2308 hypothetical protein XF2308 Q9PB37
15 1 1 15 1 XF1743 esterase est Q9PCN5
16 1 1 16 1 XF2307 hypothetical protein XF2307 Q9PB38
17 1 1 17 1 XF0272 hypothetical protein XF0272 Q9PGM6
18 1 1 18 1 XF1549 dihydrolipoamide S-succinyltransferase SUCB Q9PD30
19 1 1 19 1 XF0232 glucose-6-phosphate isomerase pgi Q9PGR6
20 1 1 20 1 XF1550 oxoglutarate dehydrogenase ODHA Q9PD29

Total number of rows: 9216

Table truncated, full table size 600 Kbytes.




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