GEO help: Mouse over screen elements for information.
Status
Public on May 29, 2007
Title
NimbleGen pathogenic virus whole-genome tiling array_Patharray2
Technology type
in situ oligonucleotide
Distribution
custom-commercial
Organism
Viruses
Manufacturer
NimbleGen Systems Inc.
Manufacture protocol
According to standard NimbleGen protocols.
Description
Pathogen detection chip Patharray2 is a tiling array covering the full genomes of 35 viruses (sequence downloaded from NCBI taxonomy webpage). Pathogen recognition signatures, comprising all probes which will hybridize to a given pathogen (including all similar probes from other pathogens which are predicted to cross-hybridize) were created. There are 7 replicates of each 40-mer probe, together with hybridization controls. The Platform data table reflects a condensed representation of the array. The complete array layout file (including the 7 replicates of each 40-mer probe) is linked as a supplementary file.
Submission date
May 11, 2007
Last update date
May 29, 2007
Contact name
Christopher Wong
E-mail(s)
wongc@gis.a-star.edu.sg
Phone
+65 6478 8103
Organization name
Genome Institute of Singapore
Street address
60 Biopolis St #02-01
City
Singapore
ZIP/Postal code
138672
Country
Singapore
Samples (40)
GSM188502 , GSM188503 , GSM188504 , GSM188505 , GSM188506 , GSM188507
GSM188508 ,
GSM188509 ,
GSM188510 ,
GSM188511 ,
GSM188512 ,
GSM188513 ,
GSM188514 ,
GSM188515 ,
GSM188516 ,
GSM188517 ,
GSM188518 ,
GSM188519 ,
GSM188520 ,
GSM188521 ,
GSM188522 ,
GSM188523 ,
GSM188524 ,
GSM188525 ,
GSM188526 ,
GSM188527 ,
GSM188528 ,
GSM188529 ,
GSM188530 ,
GSM188531 ,
GSM188532 ,
GSM188533 ,
GSM188534 ,
GSM188535 ,
GSM188536 ,
GSM188537 ,
GSM188538 ,
GSM188539 ,
GSM188540 ,
GSM188541
Series (1)
GSE7779
Optimization and Clinical Validation of a Pathogen Detection Microarray
Data table header descriptions
ID
Genome
key to identify Genome
GI
GI identifier
RANGE_GB
GenBank.version or RefSeq.version accession number
ORGANISM
Virus
RANGE_START
the start position (relative to the RANGE_GB accession)
RANGE_END
the end position (relative to the RANGE_GB accession)
ORF
open reading frame
SPOT_ID
spot identifier
Data table
ID
Genome
GI
RANGE_GB
ORGANISM
RANGE_START
RANGE_END
ORF
SPOT_ID
1-1
1
9629198
NC_001781.1
Human respiratory syncytial virus, complete genome
1
40
1-1e
1
9629198
NC_001781.1
Human respiratory syncytial virus, complete genome
6
45
1-1d
1
9629198
NC_001781.1
Human respiratory syncytial virus, complete genome
11
50
1-1c
1
9629198
NC_001781.1
Human respiratory syncytial virus, complete genome
16
55
1-1b
1
9629198
NC_001781.1
Human respiratory syncytial virus, complete genome
21
60
1-2
1
9629198
NC_001781.1
Human respiratory syncytial virus, complete genome
41
80
1-2e
1
9629198
NC_001781.1
Human respiratory syncytial virus, complete genome
46
85
1-2d
1
9629198
NC_001781.1
Human respiratory syncytial virus, complete genome
51
90
1-2c
1
9629198
NC_001781.1
Human respiratory syncytial virus, complete genome
56
95
1-2b
1
9629198
NC_001781.1
Human respiratory syncytial virus, complete genome
61
100
1-3
1
9629198
NC_001781.1
Human respiratory syncytial virus, complete genome
81
120
1-3e
1
9629198
NC_001781.1
Human respiratory syncytial virus, complete genome
86
125
1-3d
1
9629198
NC_001781.1
Human respiratory syncytial virus, complete genome
91
130
1-3c
1
9629198
NC_001781.1
Human respiratory syncytial virus, complete genome
96
135
1-3b
1
9629198
NC_001781.1
Human respiratory syncytial virus, complete genome
101
140
1-4
1
9629198
NC_001781.1
Human respiratory syncytial virus, complete genome
121
160
1-4e
1
9629198
NC_001781.1
Human respiratory syncytial virus, complete genome
126
165
1-4d
1
9629198
NC_001781.1
Human respiratory syncytial virus, complete genome
131
170
1-4c
1
9629198
NC_001781.1
Human respiratory syncytial virus, complete genome
136
175
1-4b
1
9629198
NC_001781.1
Human respiratory syncytial virus, complete genome
141
180
Total number of rows: 54117 Table truncated, full table size 4504 Kbytes .
Supplementary file
Size
Download
File type/resource
GPL5159_complete_array_layout.txt.gz
6.8 Mb
(ftp) (http)
TXT