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Status
Public on Jun 30, 2021
Title
NimbleGen Roseobacter denitrificans OCh114 12X135K array Univ. of Tokyo v2.0
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 24, 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 (8)
GSM4633796 , GSM4633797 , GSM4633798 , GSM4633799 , GSM4633800 , GSM4633801
Series (1)
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 SYMBOL DESCRIPTION CHROMOSOME Start End Strand GI
Data table ID PT_ACC GENE_ID ORF GENE SYMBOL DESCRIPTION CHROMOSOME Start End Strand GI RD1_0003
YP_680429.1
4198060
RD1_0003 aminomethyltransferase, putative
NC_008209.1
1723
2871
+
110677422
RD1_0004
YP_680430.1
4198467
RD1_0004 hypothetical protein
NC_008209.1
2948
3556
+
110677423
RD1_0005
YP_680431.1
4198468
RD1_0005 vanB
vanillate O-demethylase oxidoreductase,putative
NC_008209.1
3553
4539
+
110677424
RD1_0006
YP_680432.1
4198469
RD1_0006 hypothetical protein
NC_008209.1
4551
5618
+
110677425
RD1_0007
YP_680433.1
4198470
RD1_0007 DNA-binding protein
NC_008209.1
5659
6306
-
110677426
RD1_0008
YP_680434.1
4198471
RD1_0008 araC
AraC family transcriptional regulator
NC_008209.1
6341
7435
+
110677427
RD1_0009
YP_680435.1
4198472
RD1_0009 soxG
sarcosine oxidase, gamma subunit
NC_008209.1
7540
8100
-
110677428
RD1_0010
YP_680436.1
4198473
RD1_0010 soxA
sarcosine oxidase, alpha subunit
NC_008209.1
8093
11044
-
110677429
RD1_0011
YP_680437.1
4198474
RD1_0011 soxD
sarcosine oxidase, delta subunit
NC_008209.1
11041
11328
-
110677430
RD1_0012
YP_680438.1
4198475
RD1_0012 soxB
sarcosine oxidase, beta subunit
NC_008209.1
11341
12591
-
110677431
RD1_0013
YP_680439.1
4198476
RD1_0013 opuAC
glycine betaine transporter, substrate-bindingprotein
NC_008209.1
12850
13797
+
110677432
RD1_0014
YP_680440.1
4198477
RD1_0014 opuAA
glycine betaine transporter, ATP-bindingprotein
NC_008209.1
13879
14913
+
110677433
RD1_0015
YP_680441.1
4198478
RD1_0015 opuAB
glycine betaine transporter, permease protein
NC_008209.1
14913
16892
+
110677434
RD1_0016
YP_680442.1
4198479
RD1_0016 rluA
ribosomal large subunit pseudouridine synthaseA
NC_008209.1
16992
17639
-
110677435
RD1_0017
YP_680443.1
4198480
RD1_0017 FAD dependent oxidoreductase, putative
NC_008209.1
17670
20117
-
110677436
RD1_0018
YP_680444.1
4198481
RD1_0018 homocysteine S-methyltransferase, putative
NC_008209.1
20147
21037
-
110677437
RD1_0019
YP_680445.1
4198482
RD1_0019 dimethylglycine dehydrogenase, putative
NC_008209.1
21034
23484
-
110677438
RD1_0020
YP_680446.1
4198483
RD1_0020 hypothetical protein
NC_008209.1
23486
23650
-
110677439
RD1_0021
YP_680447.1
4198484
RD1_0021 homoserine/lactone efflux protein
NC_008209.1
23619
24242
-
110677440
RD1_0022
YP_680448.1
4198485
RD1_0022 DNA-binding protein
NC_008209.1
24239
24811
-
110677441
4129 449 Kbytes .Supplementary file Size Download File type/resource GPL28767_091016_RDKK199_Rden_60mer_expr.ndf.gz
8.1 Mb
(ftp) (http) NDF
GPL28767_091016_RDKK199_Rden_60mer_expr.ngd.gz
149.8 Kb
(ftp) (http) NGD
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