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Sample GSM4633796 Query DataSets for GSM4633796
Status Public on Jun 30, 2021
Title dnr1 mutant, denitrification_shift_1
Sample type RNA
 
Source name dnr1 mutant, denitrification_shift dark replicate 1
Organism Roseobacter denitrificans OCh 114
Characteristics genotype: dnr1 mutant
growth condition: denitrification_shift dark
Treatment protocol The culture was mixed with 2 volumes of RNAprotect Bacterial Reagent (Qiagen) before RNA purification.
Growth protocol R. denitrificans strains were cultivated aerobically in glycerol medium supplemented with 20 mM NaNO3 in a baffled Erlenmeyer flask at 30˚C with rotary shaking at 200 rpm. When optical density at 600 nm was 0.4, an aliquot of the culture was moved to a vial. After the vial was sealed with a butyl rubber septum, the headspace of the vial was replaced with argon. Total RNA was extracted after anaerobic cultivation for 3 hours.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted by a hot-phenol method. After contaminated DNA was eliminated by RQ1 DNase (Promega) treatment, RNA was purified by RNeasy mini columns (Qiagen).
Label Cy3
Label protocol Labeling of double stranded cDNA synthesized with the Superscript Double-Stranded cDNA Synthesis Kit (Invitrogen) was performed according to the instructions for NimbleGen Arrays User’s Guide for Gene Expression Analysis by Roche NimbleGen using One-Color DNA Labeling Kit (Roche NimbleGen).
 
Hybridization protocol Hybridization was performed with Hybridization System 4 according to the NimbleGen Arrays User’s Guide for Gene Expression Analysis (Roche NimbleGen).
Scan protocol Array scanning was performed with MS200 Microarray Scanner according to the NimbleGen Arrays User’s Guide for Gene Expression Analysis (Roche NimbleGen).
Description This sample is of R. denitrificans OCh114 dnr1 mutant cells after the growth condition was shifted from dark aerobic to dark denitrification. It is the first of two biological replicates used in this experiment, each from separate cultures.
Data processing The raw data (.pair file) was subjected to RMA, quantile normalization, and background correction as implemented in the NimbleScan software 2.5 (Roche NimbleGen).
 
Submission date Jun 23, 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
 
Platform ID GPL28767
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_REF
VALUE RMA-normalized, averaged gene-level signal intensity

Data table
ID_REF VALUE
RD1_0003 539.69
RD1_0004 420.175
RD1_0005 433.341
RD1_0006 320.717
RD1_0007 303.048
RD1_0008 160.835
RD1_0009 346.147
RD1_0010 238.342
RD1_0011 230.547
RD1_0012 270.194
RD1_0013 295.04
RD1_0014 297.181
RD1_0015 175.05
RD1_0016 327.798
RD1_0017 134.989
RD1_0018 152.062
RD1_0019 318.984
RD1_0020 359.555
RD1_0021 177.066
RD1_0022 292.006

Total number of rows: 4129

Table truncated, full table size 69 Kbytes.




Supplementary file Size Download File type/resource
GSM4633796_dnr1_mutant_denitrification_shift_1.pair.gz 1.9 Mb (ftp)(http) PAIR
Processed data included within Sample table

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