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Status
Public on Jun 30, 2021
Title
NimbleGen Roseobacter denitrificans OCh114 12X135K array Univ. of Tokyo v1.0
Technology type
in situ oligonucleotide
Distribution
custom-commercial
Organism
Roseobacter denitrificans OCh 114 Manufacturer
NimbleGen
Manufacture protocol
High density DNA array prepared with Maskless Array Synthesizer (MAS) technology.
Description
NimbleGen Prokaryotic Expression array (12x135K). A gene expression design for 4,129 sequences is based on the genome sequence of Roseobacter denitrificans OCh114. The length of probes is 60-mer and the number of probes is 11 pairs per gene. Each probe is replicated 3 times. Probe sequences are available in the '2009-06-23_RDKK199_Rden_60mer_expr.ndf' supplementary file.
Submission date
Jun 12, 2020
Last update date
Jun 30, 2021
Contact name
Hiroyuki Arai
Organization name
The University of Tokyo
Department
Department of Biotechnology
Lab
Lab. of Applied Microbiology
Street address
Yayoi 1-1-1
City
Bunkyo-ku
State/province
Tokyo
ZIP/Postal code
113-8657
Country
Japan
Samples (16)
GSM4613131 , GSM4613132 , GSM4613133 , GSM4613134 , GSM4613135 , GSM4613136
Series (2)
GSE152336 Transcriptome response to oxygen tension and light irradiation in Roseobacter denitrificans OCh114
GSE153074 Role of the DNR- and FNR- type regulators in regulation of the denitrification genes in Roseobacter denitrificans OCh114
Data table header descriptions ID PT_ACC GENE_ID ORF Gene name
DESCRIPTION Annotation of the target gene
Data table ID PT_ACC GENE_ID ORF DESCRIPTION RD1_0003
YP_680429.1
4198060
"aminomethyltransferase, putative"
RD1_0004
YP_680430.1
4198467
hypothetical protein
RD1_0005
YP_680431.1
4198468
vanB
"vanillate O-demethylase oxidoreductase,putative"
RD1_0006
YP_680432.1
4198469
hypothetical protein
RD1_0007
YP_680433.1
4198470
DNA-binding protein
RD1_0008
YP_680434.1
4198471
araC
AraC family transcriptional regulator
RD1_0009
YP_680435.1
4198472
soxG
"sarcosine oxidase, gamma subunit"
RD1_0010
YP_680436.1
4198473
soxA
"sarcosine oxidase, alpha subunit"
RD1_0011
YP_680437.1
4198474
soxD
"sarcosine oxidase, delta subunit"
RD1_0012
YP_680438.1
4198475
soxB
"sarcosine oxidase, beta subunit"
RD1_0013
YP_680439.1
4198476
opuAC
"glycine betaine transporter, substrate-bindingprotein"
RD1_0014
YP_680440.1
4198477
opuAA
"glycine betaine transporter, ATP-bindingprotein"
RD1_0015
YP_680441.1
4198478
opuAB
"glycine betaine transporter, permease protein"
RD1_0016
YP_680442.1
4198479
rluA
ribosomal large subunit pseudouridine synthaseA
RD1_0017
YP_680443.1
4198480
"FAD dependent oxidoreductase, putative"
RD1_0018
YP_680444.1
4198481
"homocysteine S-methyltransferase, putative"
RD1_0019
YP_680445.1
4198482
"dimethylglycine dehydrogenase, putative"
RD1_0020
YP_680446.1
4198483
hypothetical protein
RD1_0021
YP_680447.1
4198484
homoserine/lactone efflux protein
RD1_0022
YP_680448.1
4198485
DNA-binding protein
4129 256 Kbytes .Supplementary file Size Download File type/resource GPL28684_2009-06-23_RDKK199_Rden_60mer_expr.ndf.gz
7.7 Mb
(ftp) (http) NDF
GPL28684_2009-06-23_RDKK199_Rden_60mer_expr.ngd.gz
149.8 Kb
(ftp) (http) NGD
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