|
| Status |
Public on Jun 30, 2021 |
| Title |
dnr1 mutant, denitrification_shift_2 |
| Sample type |
RNA |
| |
|
| Source name |
dnr1 mutant, denitrification_shift dark replicate 2
|
| 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).
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| |
|
| 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 second 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 |
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