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Status
Public on Feb 15, 2009
Title
ULB-Erasme_MGE_Staphaureus_v2.00
Technology type
spotted oligonucleotide
Distribution
custom-commercial
Organism
Staphylococcus aureus Manufacturer
Eurogentec
Manufacture protocol
Custom made commercial DNA-microarray selectively target 403 staphylococci genes. 60-mer oligonucleotides were designed to specifically target those genes by using the Array Designer 4.0 software (Eurogentec, Liège, Belgium - www.eurogentec.com/product/research-oligonucleotide-design.html). A local BLAST database containing the eight complete S. aureus genomes was used to ensure probe specificity. Oligonucleotide probes were synthesized (http://www.eurogentec.com/product/research-oligonucleotide-synthesis-and-quality-control.html ), then printed in triplicate on UltraGaps glass slides (Corning) with the VersArray® ChipWriter Pro System (Bio-Rad)
Support
glass
Coating
aminosilane
Description
1326 probes recognize 403 target genes located on the accessory or core variable genome. Target genes encode antimicrobial resistance factors (35 %), virulence factors (28 %) and adhesins (31%).Controls:A total of 102 controls are included in the set. This encompasses:Negative controls: 84 buffer only and 6 probes corresponding to human actin and gapdh genes were positioned throughout the array to assist in determining background. Each human negative control was spotted in triplicatePositive controls: 12 probes corresponding to two distinct 23S rRNA genes and two distinct 16S rRNA genes. Each control was spotted in triplicate.
Contributor(s)
El Garch F , Hallin M , Daukandt M Submission date
Nov 20, 2008
Last update date
Feb 15, 2009
Contact name
Ricardo Luis De Mendonca
E-mail(s)
ricardo.de.mendonca@ulb.ac.be Phone
+32-2-555 8903
Fax
+32-2-555 3110
Organization name
ULB - Hôpital Erasme
Department
Microbiology
Lab
Microbiology
Street address
Route de Lennik 808
City
Brussels
ZIP/Postal code
1070
Country
Belgium
Samples (104)
GSM344538 , GSM344542 , GSM344544 , GSM344546 , GSM344548 , GSM344550
GSM344551 ,
GSM344554 ,
GSM344555 ,
GSM344556 ,
GSM344558 ,
GSM344559 ,
GSM344560 ,
GSM344561 ,
GSM344562 ,
GSM344564 ,
GSM344565 ,
GSM344566 ,
GSM344568 ,
GSM344570 ,
GSM344573 ,
GSM344575 ,
GSM344576 ,
GSM344577 ,
GSM344578 ,
GSM344580 ,
GSM511185 ,
GSM511242 ,
GSM511636 ,
GSM511637 ,
GSM512050 ,
GSM512051 ,
GSM512052 ,
GSM512053 ,
GSM512054 ,
GSM512055 ,
GSM512056 ,
GSM512057 ,
GSM512058 ,
GSM512059 ,
GSM512060 ,
GSM512061 ,
GSM512062 ,
GSM512063 ,
GSM512064 ,
GSM512065 ,
GSM512066 ,
GSM512067 ,
GSM512088 ,
GSM512089 ,
GSM512090 ,
GSM512091 ,
GSM512092 ,
GSM512093 ,
GSM512094 ,
GSM512095 ,
GSM512100 ,
GSM512101 ,
GSM512102 ,
GSM512103 ,
GSM512104 ,
GSM512105 ,
GSM512136 ,
GSM512137 ,
GSM512138 ,
GSM512139 ,
GSM512704 ,
GSM512877 ,
GSM512882 ,
GSM513055 ,
GSM515347 ,
GSM515348 ,
GSM515349 ,
GSM515519 ,
GSM515520 ,
GSM515521 ,
GSM515595 ,
GSM515596 ,
GSM515598 ,
GSM515600 ,
GSM515634 ,
GSM515635 ,
GSM516157 ,
GSM516158 ,
GSM516159 ,
GSM516160 ,
GSM516161 ,
GSM516162 ,
GSM516163 ,
GSM516164 ,
GSM516165 ,
GSM516166 ,
GSM516167 ,
GSM516168 ,
GSM516169 ,
GSM516170 ,
GSM516171 ,
GSM516172 ,
GSM516193 ,
GSM516194 ,
GSM516195 ,
GSM516196 ,
GSM516197 ,
GSM516198 Series (2)
GSE13702 StaphVar-DNA microarray analysis of accessory genome of community-acquired methicillin resistant Staphylococcus aureus
GSE20541 Livestock-associated MRSA lack accessory virulence determinants of human-associated MRSA
Data table header descriptions ID Name Oligonucleotide name
LOCUS_ID_OR_ACC_NUMBER Locus TAG number or GenBank accession number
ORF locus name in Entrez Gene
GB_ACC GenBank Accession Number
SEQUENCE Oligonucleotide probe sequence
GeneProduct Gene function description
SPOT_ID
Data table ID Name LOCUS_ID_OR_ACC_NUMBER ORF GB_ACC SEQUENCE GeneProduct SPOT_ID 1
Oligo-1
pS194_p1
pS194_p1 TTTCGTATCAGATATTGAGTATTTCACACATGAAGAAAGTTGGTTAAGTTTATTTGGAGA
Streptomycin adenylyltransferase; pfam04439
2
Oligo-1
pS194_p1
pS194_p1 TTTCGTATCAGATATTGAGTATTTCACACATGAAGAAAGTTGGTTAAGTTTATTTGGAGA
Streptomycin adenylyltransferase; pfam04439
3
Oligo-1
pS194_p1
pS194_p1 TTTCGTATCAGATATTGAGTATTTCACACATGAAGAAAGTTGGTTAAGTTTATTTGGAGA
Streptomycin adenylyltransferase; pfam04439
4
Oligo-10
SA0033
SA0033 TTCGTAATGTCTGGTCAACTTTCCGACTCTGAGAAACTTCTGGAATCGCTAGAGAATTTC
kanamycin nucleotidyltransferase
5
Oligo-10
SA0033
SA0033 TTCGTAATGTCTGGTCAACTTTCCGACTCTGAGAAACTTCTGGAATCGCTAGAGAATTTC
kanamycin nucleotidyltransferase
6
Oligo-10
SA0033
SA0033 TTCGTAATGTCTGGTCAACTTTCCGACTCTGAGAAACTTCTGGAATCGCTAGAGAATTTC
kanamycin nucleotidyltransferase
7
Oligo-100
SAUSA300_0420
SAUSA300_0420 AATTACTTAGAGCAAATATGATGACTACAAATGGAGGAGGATTATCTTCTTCGCAGCAAA
hypothetical protein
8
Oligo-100
SAUSA300_0420
SAUSA300_0420 AATTACTTAGAGCAAATATGATGACTACAAATGGAGGAGGATTATCTTCTTCGCAGCAAA
hypothetical protein
9
Oligo-100
SAUSA300_0420
SAUSA300_0420 AATTACTTAGAGCAAATATGATGACTACAAATGGAGGAGGATTATCTTCTTCGCAGCAAA
hypothetical protein
10
Oligo-101
SA0422
SA0422 TAGATCAGTATAAGAAGGCACATAAAGGAACAAAGATTTCAGCATTGAGTACAACAGTTT
hypothetical protein
11
Oligo-101
SA0422
SA0422 TAGATCAGTATAAGAAGGCACATAAAGGAACAAAGATTTCAGCATTGAGTACAACAGTTT
hypothetical protein
12
Oligo-101
SA0422
SA0422 TAGATCAGTATAAGAAGGCACATAAAGGAACAAAGATTTCAGCATTGAGTACAACAGTTT
hypothetical protein
13
Oligo-102
MW0051
MW0051 ATATTTCTGAATGTCTATATGGAGGTACAACACTAAATAGTGAAAAATTGGCACAGGAAA
enterotoxin H
14
Oligo-102
MW0051
MW0051 ATATTTCTGAATGTCTATATGGAGGTACAACACTAAATAGTGAAAAATTGGCACAGGAAA
enterotoxin H
15
Oligo-102
MW0051
MW0051 ATATTTCTGAATGTCTATATGGAGGTACAACACTAAATAGTGAAAAATTGGCACAGGAAA
enterotoxin H
16
Oligo-103
MW0755
MW0755 TTATAGAAGAGAAAGATAAACTTGAATATTACATGAAAACGGCTCAGGATAGGCTAAATT
hypothetical protein
17
Oligo-103
MW0755
MW0755 TTATAGAAGAGAAAGATAAACTTGAATATTACATGAAAACGGCTCAGGATAGGCTAAATT
hypothetical protein
18
Oligo-103
MW0755
MW0755 TTATAGAAGAGAAAGATAAACTTGAATATTACATGAAAACGGCTCAGGATAGGCTAAATT
hypothetical protein
19
Oligo-104
SAUSA300_0772
SAUSA300_0772 GATATTACGAATCAGTTGACGAATGTGACAGTTGGTATTGACTCTGGAGATACAGTTTAT
fibrinogen-binding protein
20
Oligo-104
SAUSA300_0772
SAUSA300_0772 GATATTACGAATCAGTTGACGAATGTGACAGTTGGTATTGACTCTGGAGATACAGTTTAT
fibrinogen-binding protein
1326 172 Kbytes .Supplementary data files not provided
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