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Status
Public on Dec 21, 2006
Title
Xylella fastidiosa 9a5c Biochip v.2.0
Technology type
spotted DNA/cDNA
Distribution
non-commercial
Organism
Xylella fastidiosa Manufacturer
Laboratório de Genômica Estrutural e Funcional - Núcleo Integrado de Biotecnologia - Universidade de Mogi das Cruzes
Manufacture protocol
The array consists of DNA amplicons from ~2300 ORFs from the genome of the phytobacterium Xylella fastidiosa 9a5c. The amplicons were PCR amplified with specifically designed primer pairs and purified with the QiaQuick 96 PCR purification system (Qiagen), dried in a Savant speed-vac, resuspended in 50 % DMSO at a final concentration of 100-200 mg/ml and spotted onto CMT-GAPS Coated Slides (25 x 75 mm, Corning) using an Affimetrix 427 arrayer. Those interested in obtaining the X. fastidiosa microarrays, please contact lnunes@umc.br or reginaco@umc.br for further details.
Support
glass
Coating
aminosilane
Description
Xylella fastidiosa, isolate 9a5c
Contributor(s)
Nunes LR , Oliveira RC Submission date
Dec 19, 2006
Last update date
Sep 25, 2012
Contact name
Luiz R. Nunes
E-mail(s)
luiz.nunes@ufabc.edu.br Phone
(55) (11) 4798-7104
Organization name
UFABC - Universidade Federal do ABC
Department
Centro de Ciências Naturais e Humanas
Lab
Laboratório de Genômica Funcional e Estrutural
Street address
Rua Santa Adélia 166
City
Santo André
State/province
SP
ZIP/Postal code
09210-170
Country
Brazil
Samples (68)
GSM153587 , GSM153589 , GSM153591 , GSM153592 , GSM153593 , GSM153594
GSM153595 ,
GSM153596 ,
GSM208229 ,
GSM208393 ,
GSM208395 ,
GSM208397 ,
GSM208401 ,
GSM208533 ,
GSM208535 ,
GSM208538 ,
GSM208541 ,
GSM208543 ,
GSM208545 ,
GSM208546 ,
GSM208548 ,
GSM208551 ,
GSM208554 ,
GSM208555 ,
GSM208557 ,
GSM208559 ,
GSM208563 ,
GSM208568 ,
GSM208569 ,
GSM208570 ,
GSM208571 ,
GSM208572 ,
GSM1008886 ,
GSM1008887 ,
GSM1008888 ,
GSM1008889 ,
GSM1009424 ,
GSM1009425 ,
GSM1009426 ,
GSM1009427 ,
GSM1009428 ,
GSM1009429 ,
GSM1009430 ,
GSM1009431 ,
GSM1009432 ,
GSM1009433 ,
GSM1009434 ,
GSM1009435 ,
GSM1009436 ,
GSM1009437 ,
GSM1009438 ,
GSM1009439 ,
GSM1009529 ,
GSM1009530 ,
GSM1009531 ,
GSM1009532 ,
GSM1009533 ,
GSM1009534 ,
GSM1009535 ,
GSM1009536 ,
GSM1009537 ,
GSM1009538 ,
GSM1009539 ,
GSM1009540 ,
GSM1370912 ,
GSM1370913 ,
GSM1370914 ,
GSM1370915 Series (4)
GSE6619 Transcriptome analysis of the phytobacterium Xylella fastidiosa growing under xylem-based chemical conditions
GSE8493 Comparative Genomic Analyses among Citrus-Associated strains of Xylella fastidiosa
GSE41163 Comparative Genomic Analyses among Coffee-Associated strains of Xylella fastidiosa
GSE56901 Differential gene expression in Xylella fastidiosa 9a5c during co-cultivation with the endophytic bacteria Methylobacterium mesophilicum SR1.6/6
Data table header descriptions ID ROW Row number that defines the spot position in the array
COLUMN Column number that defines spot position in the array
METAROW Metarow number that defines spot position in the array
METACOLUMN Metacolumn number that defines spot position in the array
SUBROW Subrow number that defines spot position in the array
SUBCOLUM GENOME_ACC Genome Accession Number from NCBI Entrez Genomes division
ORF Open Reading Frame (ORF) Identifier from NCBI Entrez Gene division
GENOME RANGE Genome Coordinates (in ORF number, or in Nucleotide position) for each probe spotted in the array
PROBE_ID Predicted function for the ORF spotted on the array, as verified by BLAST analyses (According to Simpson et al., 2000. Nature 406: 151-157)
CONTROL_SPOTS Positive and negative spiked controls present in the array
PRIMARY_FUNCTIONAL_CATEGORY Functional Category of the ORF spotted in the array (According to Simpson et al., 2000. Nature 406: 151-157)
SPOT_ID
Data table ID ROW COLUMN METAROW METACOLUMN SUBROW SUBCOLUM GENOME_ACC ORF GENOME RANGE PROBE_ID CONTROL_SPOTS PRIMARY_FUNCTIONAL_CATEGORY SPOT_ID 1
1
1
1
1
1
1
Lambda Q 100ng/ul
EXTERNAL CONTROL
N/A
CONTROL
2
1
2
1
1
1
2
NC_002488 Xf0065 Xf0065;
HYPOTHETICAL PROTEIN 3.7 KDA (ORF 0065)
VIII.B - Hypothetical Proteins
3
1
3
1
1
1
3
NC_002488 Xf0135 Xf0135
HYPOTHETICAL PROTEIN 7.3 KDA (ORF 0135)
VIII.B - Hypothetical Proteins
4
1
4
1
1
1
4
NC_002488 Xf0178 Xf0178
YCFJ - CONSERVED HYPOTHETICAL PROTEIN 27.8 KDA (ORF 0178)
VIII.A - Conserved Hypothetical Proteins
5
1
5
1
1
1
5
NC_002488 Xf0233 Xf0233
HI1282 - CONSERVED HYPOTHETICAL PROTEIN 23.8 KDA (ORF 0233)
VIII.A - Conserved Hypothetical Proteins
6
1
6
1
1
1
6
NC_002488 Xf0251 Xf0251
HYPOTHETICAL PROTEIN 6.4 KDA (ORF 0251)
VIII.B - Hypothetical Proteins
7
1
7
1
1
1
7
NC_002488 Xf1136 Xf1136
L1063.09 - NADP- ALCOHOL DEHYDROGENASE 38.0 KDA (ORF 1136)
I.C.2 - Intermediary Metabolism - Energy Metabolism, Carbon - Anaerobic Respiration and Fermentation
8
1
8
1
1
1
8
NC_002488 Xf0153 Xf0153
PYRE - OROTATE PHOSPHORIBOSYL TRANSFERASE 23.7 KDA (ORF 0153)
II.B.2 - Biosynthesis of Small Molecules - Nucleotides Biosynthesis - Pyrimidine Ribonucleotides
9
1
9
1
1
1
9
NC_002488 Xf1180 Xf1180
HYPOTHETICAL PROTEIN 5.2 KDA (ORF 1180)
VIII.B - Hypothetical Proteins
10
1
10
1
1
1
10
NC_002488 Xf1223 Xf1223
YADG - ABC TRANSPORTER ATP-BINDING PROTEIN 34.2 KDA (ORF 1223)
V.A.7 - Cellular Processes - Other
11
1
11
1
1
1
11
NC_002488 Xf1287 Xf1287
HYPOTHETICAL PROTEIN 15.2 KDA (ORF 1287)
VIII.B - Hypothetical Proteins
12
1
12
1
1
1
12
NC_002488 Xf1398 Xf1398
APE2426 - NA+/ H+ EXCHANGE PROTEIN 44.6 KDA (ORF 1398)
V.A.4 - Cellular Processes - Transport - Cations
13
1
13
1
1
1
13
Lambda Q 100ng/ul
EXTERNAL CONTROL
N/A
CONTROL
14
1
14
1
1
1
14
NC_002488 Xf0339 Xf0339
BTUB OR BFE OR CER- CONSERVED HYPOTHETICAL PROTEIN 97.9 KDA(ORF 0339)
VIII.A - Conserved Hypothetical Proteins
15
1
15
1
1
1
15
NC_002488 Xf0362 Xf0362
HYPOTHETICAL PROTEIN 12.0 KDA (ORF 0362)
VIII.B - Hypothetical Proteins
16
1
16
1
1
1
16
NC_002488 Xf0421 Xf0421
TTG2A - TOLUENE TOLERANCE PROTEIN 28.0 KDA (ORF 0421)
VII.G - Pathogenicity, Virulence and Adaptation - Adaptation, Atypical Conditions
17
1
17
1
1
1
17
NC_002488 Xf0462 Xf0462
HYPOTHETICAL PROTEIN 7.7 KDA (ORF 0462)
VIII.B - Hypothetical Proteins
18
1
18
1
1
1
18
NC_002488 Xf0483 Xf0483; Xf0484
HYPOTHETICAL PROTEIN 17.8 KDA (ORF 0483); HYPOTHETICAL PROTEIN 8.1 KDA (ORF 0484)
VIII.B - Hypothetical Proteins
19
1
19
1
1
1
19
NC_002488 Xf2438 Xf2438
RPSA OR SSYF - 30S RIBOSOMAL PROTEIN S1 62.9 KDA (ORF 2438)
III.B.2 - Macromolecule Metabolism - RNA Metabolism - Ribosomal Proteins
20
1
20
1
1
1
20
INTERGENIC REGION (2341007-2341233)
N/A
INTERGENIC REGION (2341007-2341233)
2688 409 Kbytes .Supplementary data files not provided
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